UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14A

(Rule 14a-101)

Proxy Statement Pursuant to Section 14(a) of the

Securities Exchange Act of 1934

Filed by the Registrant  x                             Filed by a Party other than the Registrant  ¨

Check the appropriate box:

Aegerion Pharmaceuticals, Inc.

(Name of Registrant as Specified in Its Charter)

(Name of Person Filing Proxy Statement, if Other than Registrant)

Payment of filing fee (Check the appropriate box):

April 30, 2014

Dear Stockholder:

We are pleased to invite you to attend our 2014 Annual Meeting of Stockholders, or the Annual Meeting. The Annual Meeting will be held on Wednesday, June 25, 2014, at 9:00 a.m., local time, at One Main Street, East Arcade Conference Center, Cambridge, Massachusetts 02142.

Enclosed are the following:

The Notice lists the matters to be considered at the Annual Meeting, and the proxy statement describes the matters listed in the Notice.

If you were a stockholder of record as of April 28, 2014, you will receive a printed copy of the proxy materials by mail, and you may mark, date, sign, and mail the proxy card in the envelope provided, or vote over the Internet or by telephone. You will find voting instructions in the proxy statement and on the proxy card.

If you held shares as of April 28, 2014 that were not registered in your own name, but rather were registered in the name of a bank, broker or other institution, you will receive a Notice Regarding Internet Availability of Proxy Materials with instructions that you must follow for your shares to be voted.

Your vote at the Annual Meeting is important. Whether or not you plan to attend the Annual Meeting in person, we ask that you vote as soon as possible by proxy so that your shares are represented at the Annual Meeting. We appreciate your participation and your interest in Aegerion.

NOTICE OF 2014 ANNUAL MEETING OF STOCKHOLDERS

To our Stockholders:

The 2014 Annual Meeting of Stockholders of Aegerion Pharmaceuticals, Inc., or the Annual Meeting, will be held on Wednesday, June 25, 2014, at 9:00 a.m., local time, at One Main Street, East Arcade Conference Center, Cambridge, Massachusetts 02142, for the following purposes:

These items of business are more fully described in the proxy statement accompanying this notice.

The record date for the Annual Meeting is April 28, 2014. Only stockholders of record as of the close of business on the record date are entitled to notice of, and to vote at, the Annual Meeting or any adjournments thereof.

We are mailing printed copies of our proxy materials, including our 2013 Annual Report, to stockholders of record. For stockholders who hold shares in street name through a bank, broker or other institution as of the record date, we will provide access to these materials via the Internet at www.proxyvote.com. Accordingly, on or about May 7, 2014, we will begin mailing a Notice Regarding Internet Availability of Proxy Materials to all stockholders who held shares in street name as of the record date notifying them that, among other things, they can access our proxy materials and request to receive a printed set of proxy materials at www.proxyvote.com.

WHETHER OR NOT YOU PLAN TO ATTEND THE ANNUAL MEETING IN PERSON, AND REGARDLESS OF THE NUMBER OF SHARES YOU OWN, YOUR VOTE IS VERY IMPORTANT. PLEASE VOTE AS PROMPTLY AS POSSIBLE.

Dated: April 30, 2014

AEGERION PHARMACEUTICALS, INC.

101 Main Street

Suite 1850

Cambridge, Massachusetts 02142

www.aegerion.com

PROXY STATEMENT—2014 ANNUAL MEETING OF STOCKHOLDERS

This proxy statement contains information about the 2014 Annual Meeting of Stockholders, or the Annual Meeting, of Aegerion Pharmaceuticals, Inc., a Delaware corporation, including any postponements or adjournments of the Annual Meeting. The Annual Meeting will be held on Wednesday, June 25, 2014, at 9:00 a.m., local time, at One Main Street, East Arcade Conference Center, Cambridge, Massachusetts 02142. In this proxy statement, we sometimes refer to Aegerion Pharmaceuticals, Inc. as “Aegerion,” the “Company,” “we,” “us,” or “our.”

This proxy statement contains important information for you to consider when deciding how to vote on the matters for which we are soliciting proxies. Please read it carefully.

Who Can Vote?

Only stockholders of record at the close of business on April 28, 2014, the record date, are entitled to vote at the Annual Meeting. On the record date, there were 29,482,951 shares of our common stock issued and outstanding and entitled to vote. Each share of common stock is entitled to one vote.

Stockholder of Record: Shares Registered in Your Name

If, on the record date, your shares were registered directly in your name with our transfer agent, Registrar and Transfer Company, then you are a stockholder of record, and you can vote your shares at the Annual Meeting by one of the methods described below in the section entitled “How Do I Vote and When is the Deadline for Voting?”

Beneficial Owner: Shares Registered in the Name of a Broker or Bank

If, on the record date, your shares were held in an account at a brokerage firm, bank, dealer or other similar organization, then you are the beneficial owner of shares held in “street name” and you may vote your shares at the Annual Meeting by one of the methods described below in the section entitled “How Do I Vote and When is the Deadline for Voting?”

How Will I Receive Proxy Materials?

Stockholders of Record

On or about May 7, 2014, we will mail proxy materials to your address on the records of Registrar and Transfer Company.

Hold Shares in Street Name

On or about May 7, 2014, we will begin mailing a Notice Regarding Internet Availability of Proxy Materials, or the Notice, to all stockholders who held shares in street name. We have posted our proxy materials on the website referenced in the Notice (www.proxyvote.com). You may choose to access our proxy materials on the website referenced in the Notice or may request to receive a printed set of our proxy materials by either writing to our Investor Relations Department, Aegerion Pharmaceuticals, Inc., 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142, or e-mailing Investor Relations at investorrelations@aegerion.com.

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What Proposals Will Be Presented at the Annual Meeting and What Are the Voting Recommendations of the Board of Directors?

The proposals that will be presented at the Annual Meeting and our Board of Directors’ voting recommendations are set forth in the table below:

We will also consider any other business that properly comes before the Annual Meeting. We are not currently aware of any other matters to be submitted for consideration at the Annual Meeting. If any other matters are properly brought before the Annual Meeting, one of the persons named in the enclosed proxy card will vote the shares in their discretion.

How Do I Vote and When is the Deadline for Voting?

Whether you plan to attend the Annual Meeting or not, we urge you to vote by proxy. Voting by proxy will not affect your right to attend the Annual Meeting.

Stockholder of Record

If your shares are registered directly in your name, you may vote:

Hold Shares in Street Name

If you hold shares in street name, the organization holding your account is considered the stockholder of record for purposes of voting at the Annual Meeting. The stockholder of record will provide you with instructions on how to vote your shares. Internet and telephone voting will be offered to stockholders owning shares through most banks and brokers. Additionally, if you would like to vote in person at the Annual Meeting,

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contact the broker or other nominee who holds your shares to obtain a broker’s proxy card, and bring it with you to the Annual Meeting. You will not be able to vote at the Annual Meeting unless you have a proxy card from your broker.

How Many Votes Do I Have?

Each share of common stock that you own as of the record date entitles you to one vote on each matter to be voted on at the Annual Meeting.

What If I Return a Proxy Card But Do Not Make Specific Choices?

If you return a signed and dated proxy card without marking any voting selections, your shares will be voted on the matters as recommended by our Board of Directors.

Will My Shares Be Voted if I Do Not Return My Proxy Card or Vote by the Deadline?

If you are a stockholder of record, your shares will not be voted if you do not vote using one of the methods described in the section above entitled “How Do I Vote and When is the Deadline for Voting?” in advance of the deadline.

If your shares are held in street name, and you do not provide voting instructions to the bank, broker or other nominee that holds your shares as described above under “How Do I Vote and When is the Deadline for Voting?,” the bank, broker or other nominee may exercise discretionary authority to vote on routine proposals, but may not vote on non-routine proposals. If your bank, broker or nominee votes on a routine proposal, the shares that cannot be voted on non-routine matters by the bank, broker or nominee that holds your shares are called broker non-votes. Broker non-votes will be deemed present at the Annual Meeting for purposes of determining whether a quorum exists for the Annual Meeting.

The ratification of the appointment of Ernst & Young LLP as our independent registered public accounting firm for 2014 (Proposal No. 3) is considered routine under applicable rules. The election of directors (Proposal No. 1) and the advisory vote on executive compensation (Proposal No. 2) are considered non-routine under applicable rules.

We encourage you to provide voting instructions to the bank, broker or other nominee that holds your shares. This ensures your shares will be voted at the Annual Meeting in the manner you desire.

May I Revoke My Proxy?

If you give a proxy, you may revoke your proxy at any time before the Annual Meeting in any one of the following ways:

What If I Receive More Than One Proxy Card?

You may receive more than one proxy card or voting instruction form if you hold shares of our common stock in more than one account, which may be in registered form or held in street name. Please vote in the manner described under “How Do I Vote and When is the Deadline for Voting?” for each account to ensure that all of your shares are voted.

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What Vote is Required to Approve Each Proposal?

Proposal No. 1 – the election of directors – requires an affirmative vote of a plurality of the shares of our common stock entitled to vote on the proposal that are present in person or represented by proxy at the Annual Meeting and vote for or against the proposal.

Proposal No. 2 – the advisory vote on executive compensation – requires the affirmative vote of a majority of the shares of our common stock entitled to vote on the proposal that are present in person or represented by proxy at the Annual Meeting and vote for or against the proposal. This vote is non-binding.

Proposal No. 3 – the ratification of the appointment of our independent registered public accounting firm – requires the affirmative vote of a majority of the shares of our common stock entitled to vote on the proposal that are present in person or represented by proxy at the Annual Meeting and vote for or against the proposal. This vote is non-binding. However, if stockholders fail to ratify the selection of Ernst & Young LLP, the Audit Committee of our Board of Directors, or Audit Committee, will reconsider whether or not to retain the firm for 2014. Even if the selection of Ernst & Young LLP is ratified, the Audit Committee may, in its discretion, direct the appointment of a different independent registered public accounting firm at any time during 2014 if it determines that such a change would be in the best interests of the Company and its stockholders.

What is a Quorum and How are Votes Counted?

We need a quorum of stockholders to hold our Annual Meeting. A quorum exists when at least a majority of the outstanding shares entitled to vote on the record date are represented at the meeting either in person or by proxy. Your shares will be counted towards the quorum only if a valid proxy or vote is submitted with respect to such shares. Shares represented by abstentions and broker non-votes will be counted in determining whether there is a quorum for the Annual Meeting.

Votes will be counted by the inspector of election appointed for the Annual Meeting, who will separately count “For” and “Withhold” and (with respect to proposals other than the election of directors) “Against” votes, abstentions and broker non-votes. Abstentions will have no effect on Proposal No. 1 (the election of directors), but will have the effect of a vote against Proposal No. 2 (the advisory vote on executive compensation) and Proposal No. 3 (the ratification of our independent registered public accounting firm). Broker non-votes will not be counted towards the vote total for any proposal.

Who Will Pay the Costs of Soliciting these Proxies, and How Are They Being Solicited?

Proxies are being solicited by the Company. We will pay all of the costs of soliciting the proxies described in this proxy statement. Our directors and employees may solicit proxies on our behalf in person or by telephone, fax or electronic transmission. We will not pay these directors and employees any additional compensation for these services. We will ask banks, brokers and other institutions, nominees and fiduciaries to forward these proxy materials to their principals, and to obtain authority to execute proxies, and reimburse them for their expenses. We also may utilize the assistance of third parties in connection with our proxy solicitation efforts, and we would compensate such third parties for their efforts. We have engaged one such third party, The Proxy Advisory Group, LLC, to assist in the solicitation of proxies and provide related advice and informational support, for a services fee and the reimbursement of expenses that are not expected to exceed $10,000 in the aggregate.

If you choose to access the proxy materials and/or vote on the Internet or telephonically, you are responsible for access charges you may incur.

How Can I Find Out the Results of the Voting at the Annual Meeting?

Preliminary voting results will be announced at the Annual Meeting. Final voting results will be published in a Current Report on Form 8-K to be filed with the SEC within four business days after the Annual Meeting.

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Attending the Annual Meeting

The Annual Meeting will be held on Wednesday, June 25, 2014 at 9:00 a.m., local time, at One Main Street, East Arcade Conference Center, Cambridge, Massachusetts 02142. When you arrive at the Annual Meeting location, signs will direct you to the appropriate meeting room. You should be prepared to present photo identification for admittance. In addition, if you are a stockholder of record, your name will be verified against the list of stockholders of record prior to admittance to the Annual Meeting. If you are a beneficial owner, you should provide proof of beneficial ownership on the record date, such as your most recent account statement prior to the record date, a copy of the voting instruction provided to you by your bank, broker or other nominee, or other similar evidence of ownership. You are not required to attend the Annual Meeting in order to vote.

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SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth information with respect to the beneficial ownership of our common stock as of April 15, 2014 (unless otherwise noted) with respect to:

Beneficial ownership is determined in accordance with the rules of the SEC. These rules generally attribute beneficial ownership of securities to persons who possess sole or shared voting power or investment power with respect to those securities and include shares of common stock issuable upon the exercise of stock options or other securities that are immediately exercisable or exercisable within 60 days after April 15, 2014, although these shares are not deemed outstanding for the purpose of computing the percentage ownership of any other person. Except as otherwise indicated, all of the shares reflected in the table are shares of common stock, and all persons listed below have sole voting and investment power with respect to the shares beneficially owned by them, subject to applicable community property laws. The information is not necessarily indicative of beneficial ownership for any other purpose. Percentage of ownership is based on 29,482,326 shares of common stock outstanding on April 15, 2014.

Except as otherwise indicated in the table below, addresses of named beneficial owners are c/o Aegerion Pharmaceuticals, Inc., 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142.

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BOARD OF DIRECTORS

The authorized size of our Board of Directors is seven, and we currently have seven directors in place. Our Board of Directors is divided into three classes with members of each class serving for staggered three-year terms, as follows:

Our by-laws provide that any vacancies in our Board of Directors and newly created directorships may be filled only by our Board of Directors, and that the authorized number of directors may be changed only by our Board of Directors. Any additional directorships resulting from an increase in the number of directors will be distributed among the three classes, so that, as nearly as possible, each class will consist of one-third of the total number of directors. These provisions of our by-laws and the classification of our Board of Directors may have the effect of delaying or preventing changes in the control or management of the Company.

Our Board of Directors, upon the recommendation of the Nominating and Corporate Governance Committee, or the Nominating Committee, voted to nominate Dr. Barer and Dr. Gotto for re-election as Class I directors at the Annual Meeting, for a term of three years, to serve until the 2017 Annual Meeting of Stockholders and until their respective successors have been duly elected and qualified, or their earlier resignation or removal. Our Board of Directors has determined that Dr. Barer and Dr. Gotto each possess the requisite skills, personal integrity, business judgment, industry experience and willingness to devote the time and effort necessary to serve as an effective member of our Board of Directors. A description of the background of each nominee, along with other specific experiences, qualifications, attributes or skills that contributed to the Board of Directors’ decision to nominate the nominees, is set forth below, followed immediately by similar disclosure for our existing directors whose terms of office extend beyond the Annual Meeting.

Nominees for Election at the Annual Meeting

Sol J. Barer, Ph.D. has served as a member of our Board of Directors since May 2011. Dr. Barer is currently the Managing Partner of SJBarer Consulting LLC. He previously served in various positions at Celgene Corporation (a biopharmaceutical company focused on the treatment of cancer and inflammatory diseases), including Chairman and Chief Executive Officer from May 2006 until June 2010, Executive Chairman from June 2010 until December 2010 and Non-Executive Chairman from January 2011 until June 2011. Prior to that, he held several other positions within Celgene, including President and Chief Operating Officer. Dr. Barer joined the Celanese Research Company in 1974 and formed the biotechnology group that was subsequently spun out to form Celgene. Dr. Barer currently serves on the Boards of Directors of Amicus Therapeutics (a biopharmaceutical company focused on the development of novel small molecule drugs for the treatment of genetic diseases), InspireMD, Inc. (a medical device company focused on the development and

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commercialization of stent system technology), Medgenics (a gene therapy company), RestorGenex (a biopharmaceutical company focusing on dermatology, ocular diseases, and women’s health) and several privately held biotechnology companies. Dr. Barer holds a B.S. degree from Brooklyn College and a Ph.D. degree in Organic Chemistry from Rutgers University. Our Board of Directors believes that Dr. Barer’s qualifications to sit on our Board of Directors include his significant scientific and executive leadership experience in the pharmaceutical industry.

Antonio M. Gotto, Jr., M.D., D.Phil., has served as a member of our Board of Directors since January 2006. Dr. Gotto currently serves as Co-Chairman of the Board of Overseers of the Joan and Sanford I. Weill Medical College of Cornell University and Vice President of Cornell University. From January 1997 to December 2011, Dr. Gotto served as the Stephen and Suzanne Weiss Dean of the Joan and Sanford I. Weill Medical College of Cornell University and Provost for Medical Affairs of Cornell University. Previously, Dr. Gotto served as J.S. Abercrombie Chair of Atherosclerosis and Lipoprotein Research and Chairman and Professor of the Department of Medicine at Baylor College of Medicine and Methodist Hospital. Dr. Gotto currently serves as a member of the Institute of Medicine of the National Academy of Sciences and a Fellow of the American Academy of Arts and Sciences. Dr. Gotto is also a past president of the International Atherosclerosis Society and a past president of the American Heart Association. Dr. Gotto currently serves on the Board of Directors of Esperion Therapeutics (a biopharmaceutical company focused on the development and commercialization of LDL-C lowering therapies for the treatment of hypercholesterolemia and other cardiometabolic risk markers). Dr. Gotto holds a B.A. degree from Vanderbilt University, a D.Phil. degree in Biochemistry from Oxford University in England, where he was a Rhodes Scholar, and an M.D. degree from Vanderbilt University School of Medicine. He completed his residency training at Massachusetts General Hospital in Boston, Massachusetts. Our Board of Directors believes that Dr. Gotto’s qualifications to sit on our Board of Directors include his extensive experience and expertise in the lipid area.

Directors Whose Terms Do Not Expire This Year

Marc Beer has served as our Chief Executive Officer and a member of our Board of Directors since August 2010. From November 2007 to August 2010, Mr. Beer served as a consultant and member of the boards of directors of a number of life sciences companies. From April 2000 to November 2007, Mr. Beer served as the President and Chief Executive Officer of ViaCell, Inc. (a cellular therapy company). Prior to joining ViaCell, he held marketing and business development roles at Genzyme Corporation (a biopharmaceutical company focused on the treatment of rare diseases), most recently serving as Vice President of Global Marketing. Prior to joining Genzyme, he served as Vice President, Sales and Marketing at Biostar, Inc. and held a variety of sales and marketing roles in the pharmaceutical and diagnostic devices divisions of Abbott Laboratories. Mr. Beer holds a B.S. degree from Miami University (Ohio). Our Board of Directors believes that Mr. Beer’s qualifications to sit on our Board of Directors include his extensive experience in the life sciences industry.

David I. Scheer has served as Chairman of our Board of Directors since the Company’s formation in February 2005. Since 1981, Mr. Scheer has served as President of Scheer & Company, Inc. (a company that provides venture capital, corporate strategic and transactional advisory services in the life sciences industry). Mr. Scheer serves as the Chairman of the Boards of Directors of Tengion, Inc. (a biopharmaceutical company focused on developing neo-organs) and Achillion Pharmaceuticals, Inc. (a biopharmaceutical company focused

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on the treatment of infectious diseases) and as a director of several privately held companies. Mr. Scheer is also a member of the Advisory Committee to the Harvard Malaria Initiative and the Leadership Council for the Harvard School of Public Health. Mr. Scheer holds an A.B. degree from Harvard College and an M.S. degree in cell, molecular and development biology from Yale University. Our Board of Directors believes that Mr. Scheer’s qualifications to sit on our Board of Directors include his years of experience working with life science companies.

Sandford D. Smith has served as a member of our Board of Directors since January 2012. Mr. Smith is currently a Managing Director of Tullis Health Investors, which manages a family of funds and investments focusing on the healthcare industry. Prior to joining Tullis Health Investors in January 2012, Mr. Smith served from 1996 until 2011 in various senior and executive management positions at Genzyme Corporation, including most recently as Executive Vice President and President, International Group with responsibility for the commercial activities for Genzyme’s products outside of the U.S. Prior to joining Genzyme, Mr. Smith served from 1986 to 1996 as President and Chief Executive Officer and a Director of Repligen Corporation. Mr. Smith previously held a number of positions with Bristol-Myers Squibb Company from 1977 to 1986, including Vice President of Business Development and Strategic Planning for the Pharmaceutical Group. Mr. Smith currently serves as a director of Cytokynetics, Inc. (a biopharmaceutical company) and BioBehavioral Diagnostics Company (a privately held company that manufactures and markets technologies for the diagnosis and management of neurological and psychiatric conditions), and serves as a member of the President’s Advisory Board of Brigham and Women’s Hospital in Boston. During the past five years, Mr. Smith has served as a director of Ariad Pharmaceuticals, Inc. and Nventa Biopharmaceuticals Corporation. Mr. Smith holds a B.S. degree from the University of Denver. Our Board of Directors believes that Mr. Smith’s qualifications to sit on our Board of Directors include his extensive executive experience in the life sciences industry, and in particular his experience in commercializing pharmaceutical products on a global basis, including his successful leadership at Genzyme in leading the launch of new products in various therapeutic categories, including rare diseases, on a global basis.

Paul G. Thomas has served as a member of our Board of Directors since August 2011. Mr. Thomas is the founder of Roka Bioscience, Inc. (a privately held company principally engaged in the development and commercialization of molecular assays for biopharmaceutical processing, food safety and other industrial testing applications), and since September 2009 has served as its Chief Executive Officer. From October 1998 until August 2008, Mr. Thomas served as Chairman, Chief Executive Officer and President of LifeCell Corporation (a publicly traded company that developed and marketed innovative tissue repair products for use in reconstructive, orthopedic and urogynecologic surgical procedures). LifeCell was acquired in 2008 by Kinetic Concepts, Inc. Prior to joining LifeCell, Mr. Thomas was President and Chief Operating Officer of the Pharmaceutical Products Division of Ohmeda Inc. Mr. Thomas is also a member of the Board of Directors of AbioMed, Inc. (a leading provider of medical devices that provide circulatory support to acute heart failure patients across the continuum of care in heart recovery). During the past five years, Mr. Thomas has served as a director of Orthovita, Inc. Mr. Thomas holds a B.S. degree in chemistry from St. Michael’s College in Vermont, completed his post-graduate studies in chemistry at the University of Georgia Graduate School of Arts and Science, and received an M.B.A. degree with an emphasis in Marketing and Finance from Columbia University Graduate School of Business. Our Board of Directors believes that Mr. Thomas’s qualifications to sit on our Board of Directors include his extensive executive leadership experience gained over 20 years in the life sciences industry.

Anne VanLent has served as a member of our Board of Directors since April 2013. Ms. VanLent is President of AMV Advisors, providing corporate strategy and financial consulting services to emerging growth life sciences companies. Ms. VanLent had been Executive Vice President and Chief Financial Officer of Barrier Therapeutics, Inc., a publicly traded pharmaceutical company that develops and markets prescription dermatology products, from May 2002 through April 2008. From July 1997 to October 2001, she was the Executive Vice President — Portfolio Management for Sarnoff Corporation, a multidisciplinary research and development firm. From 1985 to 1993, she served as Senior Vice President and Chief Financial Officer of The Liposome Company, Inc., a publicly-traded biopharmaceutical company. Ms. VanLent currently serves as a

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director, chair of the audit committee, and member of the nominating and governance committee of Biota Pharmaceuticals, Inc.; a director, chair of the audit committee, and chair of the nominating and governance committee of Ocera Therapeutics, Inc. (formerly Tranzyme Pharma, Inc.); and a director, chair of the audit committee, and member of the compensation committee of Onconova Therapeutics, Inc., each a NASDAQ-listed pharmaceuticals company. During the past five years, Ms. VanLent has served as a director of Integra Life Sciences Holdings, Inc., a NASDAQ-listed medical device company, where she served as chair of the audit committee from 2006 to 2012, and Penwest Pharmaceuticals Co., a NASDAQ-listed pharmaceuticals company, from 1997 until its sale to Endo Pharmaceuticals in 2010, where she served as chair of the audit committee from 2002 until 2010. Ms. VanLent received a B.A. degree in Physics from Mount Holyoke College. Our Board of Directors believes that Ms. VanLent’s qualifications to sit on our Board of Directors include her extensive leadership and finance experience, and her extensive experience serving as a board member, audit committee member and audit committee chair of public companies in the life sciences industry.

There are no family relationships among any of our directors or officers.

Director Independence

Our Board of Directors defines an independent director in accordance with the applicable provisions of the Securities Exchange Act of 1934, as amended, and regulations promulgated thereunder, or the Exchange Act, and applicable NASDAQ Marketplace Rules, or NASDAQ Rules. As a result, a director will only qualify as an “independent director” if the director meets the objective independence requirements of such laws, regulations and rules, and, in the opinion of our Board of Directors, the director does not have a relationship that would interfere with the exercise of independent judgment in carrying out the responsibilities of a director. Our Board of Directors has determined that Dr. Barer, Dr. Gotto, Mr. Scheer, Mr. Smith, Mr. Thomas and Ms. VanLent meet these requirements. Mr. Beer, who also serves as our Chief Executive Officer, is not considered independent under applicable NASDAQ Rules.

Board of Directors and Board Committee Meetings and Attendance/Annual Stockholders Meeting

Board of Directors and Board Committee Meetings

Our Board of Directors held nine meetings in 2013.

The following table and accompanying narrative provides information about the membership and meetings of the standing committees of our Board of Directors in 2013.

All of the members of these committees served on the applicable committees for all of 2013, except that in connection with Ms. VanLent’s appointment to the Board of Directors in April 2013, Ms. VanLent replaced Mr. Thomas as Chair of the Audit Committee and Mr. Scheer stepped down from the Audit Committee. During 2013, each director attended at least 75% of the meetings of our Board of Directors and the committees on which he or she served.

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The independent directors meet in executive session without management directors or management present. These sessions take place at the beginning or end of regularly scheduled meetings of the Board of Directors and most scheduled committee meetings. The independent directors met in executive session after each regularly scheduled Board of Directors meeting held during 2013.

Annual Stockholders Meetings

Our policy is to schedule a regular meeting of our Board of Directors on the same date as our annual meeting of stockholders to the extent practicable and, accordingly, directors are encouraged to be present at annual meetings of stockholders. In 2013, Mr. Beer, Mr. Scheer, Mr. Thomas and Ms. VanLent attended our annual meeting of stockholders.

Board of Directors Leadership Structure and Role in Risk Oversight

Risk is inherent with every business, and how well a business manages risk can ultimately determine its success. Our Board of Directors is actively involved in oversight of risks that could affect us. This oversight is conducted primarily through committees of our Board of Directors, as disclosed in the descriptions of each of the committees below, but the full Board of Directors has retained responsibility for general oversight of risks. Our Board of Directors satisfies this responsibility through reports by each committee chair regarding the committee’s considerations and actions, as well as through regular reports directly from officers responsible for oversight of particular risks within the Company. Our Board of Directors believes that full and open communication between management and our Board of Directors is essential for effective risk management and oversight.

We have separated the positions of Chairman of our Board of Directors and Chief Executive Officer as we believe that this allows our Chief Executive Officer to focus on our day-to-day business, while allowing the Chairman to lead our Board of Directors in its fundamental role of providing advice to and independent oversight of management. We believe that this structure ensures an enhanced role for the independent directors in the oversight of the Company and active participation of the independent directors in setting agendas and establishing priorities and procedures for the work of our Board of Directors.

Stockholder Communications with our Board of Directors

Our Board of Directors has approved a Securityholder Communication Policy that can be found on our website at www.aegerion.com. Pursuant to this policy, stockholders who wish to address questions regarding our business directly with our Board of Directors as a whole, or with any individual director, should direct his or her questions in writing to the attention of the Chairman of our Board of Directors, or an individual director, as the case may be, c/o Aegerion Pharmaceuticals, Inc., 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142. Communications will be distributed to our Board of Directors, or to any individual director or directors, as appropriate, depending on the facts and circumstances outlined in the communications.

Corporate Governance Guidelines

Our Board of Directors is committed to effective corporate governance practices. Accordingly, our Board of Directors has adopted Corporate Governance Guidelines, which describe the governance principles and procedures by which our Board of Directors functions. Among other matters, the Corporate Governance Guidelines cover director qualification standards, director responsibilities, board structure, director access to management and independent advisors, director compensation and securityholder communications with our Board of Directors. The Corporate Governance Guidelines are available on the “Corporate Governance” section of our website at www.aegerion.com.

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Code of Business Conduct

Our Board of Directors has adopted a global code of business conduct that applies to all of our employees, including our principal executive officer, our principal financial and accounting officer and our directors. The code is posted on the “Corporate Governance” section of our website at www.aegerion.com and will be made available to stockholders without charge, upon request in writing to Secretary, c/o Aegerion Pharmaceuticals, Inc., 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142. We intend to disclose on our website any amendments or waivers to the code that are required to be disclosed by SEC rules.

Board Committees

Our Board of Directors has established an Audit Committee, a Compensation Committee and a Nominating Committee. Each of these committees operates pursuant to a separate written charter adopted by our Board of Directors. The charters of the Audit Committee, Compensation Committee and Nominating Committee are available on the “Corporate Governance” section of our website at www.aegerion.com.

The composition and functioning of all of our committees comply with all applicable requirements of the Sarbanes-Oxley Act of 2002, the NASDAQ Rules and SEC rules and regulations.

Audit Committee

Mr. Smith, Mr. Thomas and Ms. VanLent currently serve on the Audit Committee, with Ms. VanLent serving as the Audit Committee’s chair. Our Board of Directors has determined that Mr. Smith, Mr. Thomas and Ms. VanLent each qualify as an “audit committee financial expert” for purposes of the Exchange Act.

Our Board of Directors has also determined that each of Ms. VanLent, Mr. Smith and Mr. Thomas is an independent director under the applicable NASDAQ Rules and Rule 10A-3 of the Exchange Act.

The Audit Committee’s responsibilities include, among other things:

Compensation Committee

Dr. Barer and Mr. Scheer currently serve on the Compensation Committee of our Board of Directors, or the Compensation Committee, with Dr. Barer serving as the Compensation Committee’s chair. Our Board of Directors has determined that each of Dr. Barer and Mr. Scheer is an independent director under the applicable NASDAQ Rules, a non-employee director under Rule 16b-3 of the Exchange Act and an outside director for the purposes of Section 162(m) of the Internal Revenue Code of 1986, as amended, or the Code. The Compensation Committee’s responsibilities include, among other things:

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Nominating Committee

Dr. Barer, Dr. Gotto and Mr. Scheer currently serve on the Nominating Committee with Dr. Gotto serving as the Nominating Committee’s chair. Our Board of Directors has determined that each of Dr. Barer, Dr. Gotto and Mr. Scheer is an independent director under the applicable NASDAQ Rules. The Nominating Committee’s responsibilities include, among other things:

Compensation Committee Interlocks and Insider Participation

None of our executive officers serves as a member of the Board of Directors or the Compensation Committee, or other committee serving an equivalent function, of any other entity that has one or more of its executive officers serving as a member of our Board of Directors or on our Compensation Committee. None of the members of our Compensation Committee has ever been one of our employees.

Director Nominations and Qualifications

As it becomes necessary to fill one or more seats on our Board of Directors, the Nominating Committee will consider in a timely fashion potential candidates for director who have been recommended by our directors, Chief Executive Officer, other members of senior management or stockholders. The procedures for submitting stockholder nominations are explained under “Stockholder Proposals” elsewhere in this proxy statement. The Nominating Committee may also engage a third-party search firm to identify potential director candidates for its consideration, or use any other source it deems appropriate for identifying candidates for director. To fill the seat on our Board that was eventually filled by Ms. VanLent, the Nominating Committee retained Russells Reynolds Associates, a global executive search firm, to develop a list of candidates who possessed the background, experience, and qualifications to serve on our Board of Directors. A successful search resulted in Ms. VanLent being selected to join our Board of Directors.

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The Nominating Committee will meet as often as it deems necessary to narrow the list of potential candidates, review any materials provided in connection with potential candidates and cause appropriate inquiries to be conducted into the backgrounds and qualifications of each candidate. The Nominating Committee recommends to our Board of Directors the candidates that it feels should be nominated for election by the stockholders or named by our Board of Directors to fill a vacancy.

The Nominating Committee evaluates each individual candidate in the context of overall composition and needs of our Board of Directors, with the objective of recommending a group that can best manage the business and affairs of the Company and represent stockholder interests. The Nominating Committee seeks to achieve a mix of board members representing a diversity of backgrounds and experience. The Nominating Committee must be satisfied that each recommended nominee meets the following minimum qualifications:

Finally, in addition to any other standards the Nominating Committee may deem appropriate from time to time for the overall structure and composition of our Board of Directors, the Nominating Committee may consider the following factors when selecting and recommending that our Board of Directors select persons for nomination: whether the nominee, if elected, assists in achieving a mix of members that represents a diversity of background and experience and whether the nominee is well regarded in the community. The Nominating Committee has not adopted a formal policy with regard to the consideration of diversity in identifying director nominees. However, the Nominating Committee may consider the diversity of background and experience of a director nominee in the context of the overall composition of our Board of Directors at that time, such as diversity of knowledge, skills, experience, geographic location, age, gender, and ethnicity.

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DIRECTOR COMPENSATION

Non-Employee Director Compensation Policy

Our Board of Directors has adopted a Non-Employee Director Compensation Policy that sets forth the cash payments and other forms of compensation that each non-employee director receives for serving as a member of our Board of Directors and its committees. Mr. Beer, our Chief Executive Officer, does not receive any separate compensation for serving on our Board of Directors. The compensation he earned in his capacity as Chief Executive Officer is included in the Summary Compensation Table found in the “Executive Compensation” section of this proxy statement.

Our Non-Employee Director Compensation Policy is designed to provide a total compensation package for non-employee directors that enables us to attract and retain, on a long-term basis, high-caliber non-employee directors and to align the directors’ interests with the long-term interests of our stockholders.

Cash Compensation

Below is a summary of cash compensation payable to non-employee directors in 2013:

The annual retainers are paid quarterly, in arrears. Upon the resignation or removal of a non-employee director, his or her annual retainers are pro-rated based on the number of calendar days served by such director in the applicable period.

Equity Awards

Under our Non-Employee Director Compensation Policy, the Compensation Committee grants equity awards to non-employee directors as follows:

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Except as provided below, so long as the director remains on our Board of Directors, his or her initial option grants will vest in equal annual installments over three years beginning on the first anniversary of the date of grant, and annual option grants will vest in their entirety on the first anniversary of the date of grant.

Director option grants will become immediately exercisable upon the death, disability or retirement of a director or upon a change in control of the Company. Directors will have up to three years following cessation of service as a director to exercise their options (to the extent vested at the date of such cessation), provided that the director has not been removed for cause. All of the foregoing options will be granted with an exercise price equal to the fair market value of a share of our common stock on the date of grant.

Director Compensation Table

The following table sets forth a summary of the compensation earned by our non-employee directors in 2013. We have intentionally omitted columns from this table pertaining to types of compensation not paid to our non-employee directors in 2013.

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EXECUTIVE OFFICERS

The following table sets forth the name, ages and positions of our current executive officers as of April 15, 2014:

Mark Fitzpatrick has served as our Chief Financial Officer since May 2011. From July 2007 to May 2011, Mr. Fitzpatrick served as Vice President and Chief Financial Officer of Proteon Therapeutics, Inc. (a privately held biopharmaceutical company engaged in the development of products to treat renal and vascular diseases). From August 2005 to May 2007, Mr. Fitzpatrick was Vice President, Chief Financial Officer, Treasurer and Assistant Secretary of RenaMed Biologics, Inc. Mr. Fitzpatrick previously held Chief Financial Officer positions with Dynogen Pharmaceuticals, Worldstreet Corporation and Diacrin, Inc. Prior to those positions, Mr. Fitzpatrick held various financial management positions with Repligen Corp. and was a senior auditor with Arthur Andersen & Co. Mr. Fitzpatrick holds a B.S. degree from Boston College and a was awarded a CPA certificate from the Commonwealth of Massachusetts in 1987.

Martha Carter has served as our Chief Regulatory Officer and Senior Vice President since February 2011. From January 2011 to February 2011, Ms. Carter served as Senior Vice President and Chief Regulatory Officer at Proteon Therapeutics, Inc. (a privately held biopharmaceutical company), and from September 2006 to December 2010, she served as Senior Vice President, Regulatory Affairs and Quality Assurance, at Proteon. In both roles, Ms. Carter was responsible for Proteon’s worldwide regulatory and quality functions. From September 2002 to April 2006, Ms. Carter was Senior Vice President, Regulatory Affairs, for Trine Pharmaceuticals. Prior to joining Trine, Ms. Carter was Vice President, Regulatory Affairs for GelTex Pharmaceuticals, Inc. Ms. Carter holds a B.A. degree from Northeastern University.

Anne Marie Cook has served as our Senior Vice President, General Counsel and Secretary since December 2011. From December 2008 to December 2011, Ms. Cook was a partner at the law firm Choate Hall & Stewart LLP, where she represented both private and public corporations in the life sciences industry in structuring and negotiating strategic transactions and providing general legal support in connection with the research, development and commercialization of pharmaceutical products. From April 2007 to December 2008, Ms. Cook was a Principal at the law firm Miller Canfield P.L.C. From September 2005 until April 2007, Ms. Cook served as General Counsel and Senior Vice President, Business and Corporate Development, and Secretary of ViaCell, Inc. (a biotechnology company). Prior to joining ViaCell, Ms. Cook spent thirteen years at Biogen Idec Inc., most recently as Vice President, Chief Corporate Counsel. Ms. Cook holds a B.S. degree from Tufts University and a J.D. degree from the University of Notre Dame Law School.

Craig Fraser has served as our President, U.S. Commercial & Global Manufacturing and Supply Chain since September 2012. From October 2011 to September 2012, Mr. Fraser served as our President, U.S. Before joining the Company, Mr. Fraser was Vice President, Global Disease Areas at Pfizer Inc. (a global pharmaceutical company) from November 2009 to August 2011, where he was responsible for the commercial development and global marketing for the Specialty Cardiovascular, Anti-Bacterial, Anti-Fungal,

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Gastrointestinal and Anti-Viral disease areas, and managed a portfolio of six products totaling over $3 billion in revenue and multiple new products in development. Prior to joining Pfizer, Mr. Fraser was Vice President and Global Business Manager at Wyeth (a pharmaceutical company) from December 2007 to November 2009, where he led the institutional/infectious disease business. Before that, Mr. Fraser held several commercial positions at Johnson & Johnson, most recently as Vice President, Commercial Operations and Oncology Sales and Marketing. Previously, he was Gastroenterology Franchise lead as well as National Sales Director of the Immunology and Cardiovascular business units at Centocor, a start-up biotech and diagnostic company focused on monoclonal antibody-based technology. Mr. Fraser holds a B.S. degree from Slippery Rock University.

Mark Sumeray has served as our Chief Medical Officer since August 2011. From November 2009 to July 2011, Dr. Sumeray served as Vice President, Cardiovascular/Metabolics U.S. Medical at Bristol-Myers Squibb (a pharmaceutical company). From December 2004 to November 2009, Dr. Sumeray held various positions at The Medicines Company, including Vice President and Business Unit Co-Leader, Vice President, Medical Business Development, and Vice President Clinical Development and Head of Medical Science. From September 2000 to October 2004, Dr. Sumeray served as worldwide Vice President of Clinical Development for the Ethicon Franchise of Johnson & Johnson. Dr. Sumeray holds a B.S. degree, an M.S. degree in surgery and an M.D. degree from the University College London. Dr. Sumeray is a Fellow of the Royal College of Surgeons, or FRCS, in the United Kingdom.

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EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

This Compensation Discussion and Analysis provides an overview and analysis of the compensation philosophy of the Company, our compensation programs, the decisions we made in 2013 under those programs with respect to our named executive officers, and the factors we considered in making those decisions. We also address certain compensation programs we have implemented in 2014 for our named executive officers. This discussion is intended to help our stockholders understand the detailed information provided in the compensation tables included in this proxy statement, and to put that information in the context of our overall compensation program.

Our “named executive officers” for 2013 are:

Overview of 2013 Company Performance

We achieved strong performance in 2013, which built on our significant accomplishments in 2012. Highlights of our 2013 performance include the following accomplishments:

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In 2012, we had a number of major accomplishments, including the following:

Overview of Our Executive Compensation Objectives and Pay-for-Performance Philosophy

Our compensation programs are designed to:

To achieve these objectives, we seek to provide a competitive total compensation package, a substantial portion of which is tied to the achievement of our corporate goals and the executive’s individual performance.

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The key elements of the performance-based compensation provided to our named executive officers are our equity program, which includes both annual grants and awards under our Long Term Incentive Program, or LTIP, and our annual cash incentive program. Our equity program, including our LTIP, focuses exclusively on our long-term performance and delivering stockholder value, while our annual cash incentive program focuses on our short-term performance in key areas that are ultimately needed to drive our long-term success. All equity compensation for our named executive officers, including our LTIP, has been delivered in the form of stock options to date. A substantial percentage of the total direct compensation (i.e., base salary, annual cash incentive bonus, and long-term equity incentives) of our named executive officers is delivered as performance-based compensation. Approximately 90% of the total direct compensation paid to our CEO, and approximately 80% of the total direct compensation paid to our other named executive officers, is in the form of performance-based cash and equity compensation. We believe that the emphasis on equity-based compensation and annual cash incentives is consistent with our pay-for-performance philosophy and appropriately balances incentives to achieve long-term delivery of stockholder return with incentives to achieve our annual operating objectives. For 2013, our named executive officers’ total compensation was distributed among the three main elements of our compensation – base salary, annual cash short-term incentive bonus, or STI, and long-term equity incentives, or LTI – as follows:

We establish our target total direct compensation at levels we believe will reward and incentivize value creation for the Company. We targeted our total direct compensation at the 50^th percentile in 2012 relative to our peer group and similar companies as shown on the Radford Global Life Sciences Survey. As we began significant growth globally, in order to attract and retain key talent with the experience and capabilities needed, our compensation philosophy evolved in 2013 to target base salaries at the 50^th percentile and to target annual cash incentive bonus and the grant date value of equity awards at the 50^th to 75^th percentile, in each case relative to our peer group and similar companies as shown on the Radford Global Life Sciences Survey, as discussed in more detail below.

Compensation Framework: Policies and Process

Roles of Compensation Committee and Chief Executive Officer in Compensation Decisions

The Compensation Committee oversees our total compensation philosophy, compensation programs, equity incentive programs and benefit plans, and annually reviews and approves all compensation decisions relating to our Chief Executive Officer and all other named executive officers. Our Board of Directors typically reviews and approves the compensation decisions made by the Compensation Committee with respect to Mr. Beer, our Chief Executive Officer. Mr. Beer provides recommendations to the Compensation Committee with respect to salary adjustments, annual cash incentive bonus targets and awards and equity incentive awards for our named executive officers (other than himself) and the other executive officers reporting to him. In making compensation decisions relating to the named executive officers other than Mr. Beer, the Compensation Committee takes into account Mr. Beer’s recommendations. The Compensation Committee, as the ultimate body that approves the compensation of our named executive officers, has the discretion to increase or decrease the amounts of

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compensation recommended by Mr. Beer. The Compensation Committee also reviews our named executive officers’ base salary increases based on an assessment of the executive’s individual performance and contribution to our corporate performance and achievements, as well as benchmarking data. Annual bonus payments are determined based on actual corporate and individual performance against goals. The size of both annual equity awards and equity awards made under our LTIP for our named executive officers is determined based on each individual’s contribution to our overall corporate achievement, their individual performance, and benchmarking data. All compensation decisions are assessed within the framework of our financial position and general economic conditions.

Competitive Market Data and Use of Compensation Consultant

We use both internal and external benchmarking to assist us in making compensation decisions for our named executive officers. We benchmark annually our target total direct compensation and each primary element of our named executive officers’ compensation – base salary, target annual cash incentive compensation and target long-term equity incentive compensation, including annual and LTIP awards – against a set of peer group companies that the Compensation Committee reviews each year (as described further below) in order to ensure that our compensation programs are within the competitive range of comparable companies, and the Radford Global Life Sciences Survey, which includes public biopharmaceutical companies with between 30 and 300 employees. The Radford Global Life Sciences Survey provides us with data on the compensation of executives at companies within our peer group and at other similar companies. We also benchmark internally to ensure that the target compensation of each of our named executive officers is established equitably and based on their actual, and anticipated future, contributions to the Company’s performance.

Since 2011, the Compensation Committee has engaged Radford, an Aon Hewitt company, as its outside compensation consultant. The Compensation Committee assessed the independence of Radford pursuant to the SEC rules, and has concluded that no conflict of interest exists that would prevent Radford from independently representing the Compensation Committee. Radford was selected and retained by the Compensation Committee to provide advice regarding our executive compensation programs, including:

In reviewing compensation levels of our named executive officers for 2013, Radford assisted us in an analysis of competitive market data. Data sources included public company proxy statements and the Radford Global Life Sciences Survey, as described above. The benchmarking we obtained from Radford was used to determine our competitive position among similarly-situated companies in the marketplace, and to set our targeted pay at a competitive range relative to our peer group and other similar companies in 2013 for base salary at the 50th percentile, and for target annual cash incentive bonus and equity-based awards at the 50th to 75th percentile in order to enable us to attract and retain top talent. The Compensation Committee sets actual compensation for our named executive officers based on this benchmarking data and the Compensation Committee’s assessment of the role and impact of each executive and his or her individual performance.

On an annual basis, Radford recommends, and the Compensation Committee approves, a group of comparable companies as our peer group. Our peer group for 2013 compensation was approved by the Compensation Committee in October 2012 and our peer group for 2014 compensation was approved by the Compensation Committee in October 2013. Each of these peer groups is listed in the table below. The primary reason for the changes to our peer group from 2013 to 2014 was the evolution of our business profile as we experienced significant global growth as a commercial organization. As a result, the Compensation Committee believed that we should adjust our peer group to include comparable companies with commercial products and market capitalizations closer to our average market capitalization at the time of the 2014 peer group selection.

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Both our 2013 and 2014 peer groups were selected on the basis of similarity to the Company at the time of selection based on the following criteria: business comparability, stage of product development, number of employees, market capitalization, financial profile and, to some degree, similarity of product or therapeutic focus.

The 2013 peer group was used to establish the 2013 compensation for our Chief Executive Officer and the other named executive officers, as set forth in the Summary Compensation Table immediately following this Compensation Discussion and Analysis section.

Corporate Governance

Our compensation practices emphasize good governance and market practice. To this end:

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Executive Compensation Components

Our executive compensation consists of the following components:

Below we discuss each element of our executive compensation, how it fits into our overall executive compensation philosophy, and the amounts of each element of compensation paid to or earned by our named executive officers in 2013.

Although we have not yet adopted any formal guidelines for allocating total compensation between long-term and short-term incentive compensation and between cash and non-cash compensation, or among different forms of non-cash compensation, our compensation programs tie a substantial portion of our named executive officers’ overall compensation to the achievement of both short- and long-term corporate goals and key performance milestones.

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2013 Compensation

Our 2013 compensation decisions reflect the performance of our named executive officers in achieving our performance goals in 2012 and 2013, including those set forth above under “Overview of Compensation and Company Performance.”

Base Salary

The Compensation Committee establishes base salary levels and increases with the objective of providing base salaries generally at the 50th percentile relative to our peer group and similarly-situated companies based on the Radford Global Life Sciences Survey. The base salaries of our named executive officers are reviewed annually, and adjusted to reflect individual roles, experience, capability, scope of responsibility, and performance during the year, the impact of the executive’s performance on our overall performance, and the Radford benchmarking data.

The base salaries of our named executive officers during 2012 and 2013 are set forth in the table below.

In 2013, the base salary of each named executive officer was increased as follows based on an assessment by the Compensation Committee (and Mr. Beer, in the case of the other named executive officers) of the executive’s performance and the scope and impact of the executive’s role (referred to as the merit increase below) and to reflect market compensation more closely (referred to as the market adjustment below).

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Performance-Based Short-Term Incentive Compensation

The Compensation Committee has the authority to award annual performance-based cash bonuses to our named executive officers. The target cash bonus percentages for the named executive officers in 2013, as a percentage of base salary, were as follows:

The actual bonus awards are determined based on the level of achievement against annual corporate and individual goals. Payments are made in cash. The corporate goals are set by our Board of Directors as guided by the Compensation Committee. The Compensation Committee has the discretion to award cash bonuses that are greater than or less than a named executive officer’s target bonus amount, depending on the level of achievement of corporate or individual performance goals. The maximum payout level under the corporate goals is 150% of target.

The bonus payments made to our named executive officers for 2013 were based on the achievement of corporate and individual goals, with 80% of the bonus tied to achievement of corporate goals and 20% tied to achievement of individual goals, except for Marc Beer, our Chief Executive Officer, whose bonus is tied 100% to achievement of corporate goals.

Our approved 2013 corporate goals consisted of:

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In determining our corporate performance score each year, the Compensation Committee may also elect to consider our overall performance in addition to our level of achievement against approved corporate performance goals for the relevant year. The Compensation Committee determined our corporate performance score of 150% for 2013 based solely on the Compensation Committee’s assessment of our level of achievement against our approved 2013 corporate performance goals set forth above.

As noted above, 20% of the performance bonus of each named executive officer, other than Mr. Beer, is measured by reference to achievement of individual performance goals. The Compensation Committee, however, concluded that in 2013 each of these named executive officers fully met or exceeded their individual performance goals. The individual performance goals in 2013 for each of the named executive officers, other than Mr. Beer, and the weight attributed to each goal, are described below:

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Based on the corporate goal score of 150% and, except for Mr. Beer, the level of achievement against individual goals, the Compensation Committee awarded cash bonuses for 2013 to the named executive officers, as follows:

Long-Term Incentives (Stock Options)

We have a broad-based equity compensation program designed to reward and motivate our employees, including our named executive officers. Equity awards help align the interests of our named executive officers and other employees with the long-term interests of our stockholders, and provide an opportunity for employees to acquire ownership in the Company.

New Hire and Annual Awards

Each of our named executive officers received stock options in connection with his or her hire and upon promotion, as applicable. Our named executive officers are also eligible to receive annual stock option grants in an amount commensurate with individual and corporate performance and with the grant date value benchmarked at the 50^th to 75^th percentile relative to our peer group and similar companies as shown on the Radford Global Life Sciences Survey. These stock option awards provide our named executive officers with the right to purchase shares of our common stock at a fixed exercise price, subject to continued employment with our Company. Stock options granted prior to October 2013 generally vest over four years in equal monthly installments commencing immediately after the date of grant. In October 2013, we revised the vesting schedule for stock option grants to new hires and for annual grants to existing employees to provide that stock options granted on or after October 1, 2013 generally vest as to 25% of the options on the first anniversary of the grant date and vest in equally monthly installments as to the remaining shares until fully vested. Performance-based stock option awards generally vest immediately after the achievement of specific milestone events. We consider time-vesting stock options to be performance-based because no value is created unless the value of our common stock appreciates after grant.

Performance-Based Long-Term Incentive Plan

In 2012, we implemented the LTIP to align the focus of our executive team with the interests of our stockholders in achieving long-term value by providing incentive awards based on achievement of long term, pre-established corporate milestones and goals. The LTIP complements our annual cash compensation program and annual stock option grants by ensuring our executives remain focused on delivering long-term value and achieving established performance goals when making key decisions. The program is also designed to assist in retaining key executives critical to our long-term success. The LTIP, and the awards made pursuant to it, are subject to the terms of our 2010 Stock Option and Incentive Plan, or 2010 Option Plan. Each performance cycle

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under the LTIP is three years. The options granted in the 2012 – 2014 performance cycle will vest at the end of such cycle if the performance goals are obtained, and the options granted in the 2013 – 2015 performance cycle will vest as to the number of shares of stock, if any, that corresponds to the Company’s level of achievement against the performance goals applicable to such cycle. As of December 31, 2013, we had granted awards for the 2012 – 2014 and 2013 – 2015 performance cycles. The performance cycle awards for each cycle consist of stock options granted at the commencement of the relevant plan cycle that will vest upon the achievement of the performance goals specified in each LTIP award. The performance goals for the LTIP awards that cover 2012 through 2014 consist of cumulative net revenues, average market capitalization and regulatory approvals of lomitapide. The performance goals for the LTIP awards that cover 2013 through 2015 consist of net revenues, average market capitalization, the number of revenue-generating countries in 2015 and clinical development of lomitapide. These specific goals were chosen due to their impact on our profitability and our ability to obtain regulatory approvals for lomitapide in additional key markets.

The Compensation Committee establishes, selects and determines the program participants, the three-year performance goals and the type and amount of the incentive award tied to the performance goals. Our Chief Executive Officer and all executives who directly report to our Chief Executive Officer, including our named executive officers, participate in the program, and the Compensation Committee may also include other executives or members of senior management whose role or achievement in key areas is critical to ensure delivery of stockholder value. The level of achievement of our performance-based awards, including performance-based options, will be determined by an objective formula meeting the requirements of the LTIP Plan and consistent with the 2010 Option Plan. In the event of a sale event as defined in the 2010 Option Plan, the vesting of performance-based options/shares held by our named executive officers will be treated like all other equity awards in accordance with the terms of their respective employment agreements, the 2010 Option Plan, or other award documents, but may also be accelerated at the discretion of the Compensation Committee.

Long-Term Incentive Award Determinations

In making grant decisions relating to our named executive officers, the Compensation Committee utilizes competitive market data provided by Radford to target a grant date value at the 50^th to 75^th percentile relative to our peer group and similar companies as shown on the Radford Global Life Sciences Survey for the executive’s position and also considers the executive’s level and scope of responsibility and potential contribution to the advancement of our corporate objectives. Typically, larger awards have been made to the named executive officers with the roles and responsibilities that are more likely to build long-term stockholder value through their potential to contribute to our growth and to help us achieve key milestones.

In 2013, the Compensation Committee made the following option grants to our named executive officers:

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Equity Grant Approvals/Timing

All grants to our named executive officers must be approved by the Compensation Committee. The Compensation Committee has delegated authority to our Chief Executive Officer to grant stock options to employees other than executive officers based on a budget and guidelines approved by the Compensation Committee and consistent with our overall compensation philosophy. All stock options are awarded with an exercise price equal to fair market value of a share of common stock on the date of grant calculated based on the closing market price of our common stock on such date. The grant date of equity awards will typically be determined on a regularly scheduled basis, as follows:

See “Potential Payments upon Termination or Change-in-Control” for a discussion of the change-in-control provisions related to stock options held by our named executive officers.

Other Compensation

Broad-based benefit programs. We currently maintain broad-based benefits and perquisites that are provided to all full-time employees, including our named executive officers, including health insurance, life and disability insurance, dental and vision insurance and a 401(k) plan.

Our 401(k) plan is intended to qualify under Section 401 of the Code. Our 401(k) plan permits employees to make contributions up to the statutory limit. We have the discretion to match up to 50% of the first 6% of gross wages that an employee contributes, resulting in a maximum match by us that totals up to 3% of an employee’s gross wages (as further limited by statutorily defined annual compensation limits). We did match employee contributions in 2013.

Certain personal benefits. We generally provide relocation, commuting and related benefits to our named executive officers who do not live in the Cambridge, Massachusetts area when they are hired.

Pursuant to his employment agreement, we provided Dr. Sumeray with a housing allowance towards the rental of an apartment in the Cambridge, Massachusetts area and to offset his associated tax liability related to such housing allowance. The amount of this allowance, including the cost to offset the associated tax liability, was $5,145 per month. We also agreed to reimburse Dr. Sumeray for his reimbursable travel expenses directly related to his commuting to our Cambridge offices and to offset his associated tax liability up to a maximum of 40% of the aggregate amount of such expenses, on a quarterly basis. We agreed to provide these benefits through December 31, 2013 and, after that, to cover reasonable expenses related to his relocation to Cambridge.

Severance and change-in-control payments/benefits. As discussed below in “Employment Agreements and Severance Agreements with Named Executive Officers” and in “Potential Payments Upon Termination or Change-in-Control,” we have agreements with our named executive officers providing certain severance benefits to them upon termination of their employment or in connection with a change in control of the Company, including the acceleration of vesting of then outstanding unvested equity awards. Our goal in providing severance and change in control benefits is to offer sufficient protection such that a named executive officer will devote his or her full time and attention to the requirements of the business rather than to the potential implications for his or her position. We prefer to have certainty regarding the potential severance amounts payable to our named executive officers under certain circumstances, rather than negotiating severance at the time that a named executive officer’s employment terminates. We have also determined that accelerated vesting

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provisions in connection with a termination following a change in control are appropriate because such provisions will encourage our executives holding unvested equity awards, including our named executive officers, to stay focused on their responsibilities in such circumstances, rather than be distracted by the potential implications for them of the change in control.

Say-on-Pay Consideration

We provide our stockholders with the opportunity to cast an advisory vote, once every three years, to approve the compensation of our named executive officers (commonly referred to as “Say-on-Pay”). The last such advisory Say-on-Pay vote took place at our annual meeting of stockholders held in June 2011, at which a substantial majority (96.2%) of the votes cast on the proposal at that meeting voted in favor of approving the overall compensation of our named executive officers and our compensation philosophy, policies and practices. The Compensation Committee believes the results of that advisory Say-on-Pay vote affirm stockholders’ support of our approach to executive compensation, and we have not implemented any changes as a direct result of the vote. The Compensation Committee continues to review, assess and adjust our named executive officers’ compensation on a regular basis to best position the Company to achieve its compensation objectives. We expect that the Compensation Committee will continue to consider the outcome of advisory votes on executive compensation, including this year’s vote, when making future compensation decisions with respect to our named executive officers.

Section 162(m) of the Internal Revenue Code and Accounting Considerations

We consider the tax and accounting rules associated with various forms of compensation when designing our compensation programs. However, to maintain flexibility to compensate our named executive officers in a manner designed to promote our long-term corporate goals and objectives, the Compensation Committee has not adopted a policy that all compensation must be deductible or have the most favorable accounting treatment to the Company.

Section 162(m) of the Code limits to $1 million the amount a company may deduct for compensation paid to its chief executive officer and any of its other three named executive officers (excluding the chief financial officer). This limitation does not, however, apply to compensation meeting the definition of “qualifying performance-based compensation.” The Compensation Committee believes that its primary responsibility is to provide a compensation program that attracts, retains and rewards the executive talent necessary for our success. Consequently, the Compensation Committee may pay or provide, and has paid or provided, compensation in excess of $1 million that is not exempt from the deduction limitations under Section 162(m). The stock options granted to our named executive officers were intended to be tax-deductible compensation under Section 162(m). Our annual cash incentive awards, as currently structured, are not considered performance-based for purposes of Section 162(m). Therefore, the value of those bonuses, in combination with the amount of salary and certain other elements of compensation, in excess of $1 million paid to our Chief Executive Officer or any of our three highest paid executive officers, other than our Chief Executive Officer and our Chief Financial Officer, is not tax deductible by us.

The Compensation Committee considers the accounting implications of significant compensation decisions, especially in connection with decisions that relate to our equity incentive award plans and programs. As accounting standards change, we may revise certain programs to appropriately align accounting expenses of our equity awards with our overall executive compensation philosophy.

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Compensation Committee Report

The Compensation Committee has reviewed and discussed with management the foregoing Compensation Discussion and Analysis required by Item 402(b) of Regulation S-K. Based on this review and discussion, the Compensation Committee has recommended to our Board of Directors that the Compensation Discussion and Analysis be included in this proxy statement and our Annual Report on Form 10-K for 2013.

By the Compensation Committee of the Board of Directors of Aegerion Pharmaceuticals, Inc.

Sol J. Barer, Ph.D., Chairman

David I. Scheer

This report shall not constitute “soliciting material,” shall not be deemed “filed” with the SEC and is not to be incorporated by reference into any of our other filings under the Securities Act of 1933, as amended, or the Securities Act, or the Exchange Act, except to the extent that we specifically incorporate this report by reference therein.

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Executive Compensation Tables

Summary Compensation

The information included in the Summary Compensation Table below reflects compensation earned, if applicable, during each of the last three years by our named executive officers.

Summary Compensation Table

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Grants of Plan-Based Awards

The following table sets forth certain information with respect to awards under our non-equity and equity incentive plans made to our named executive officers during 2013.

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Outstanding Equity Awards at Year-End

The following table sets forth certain information with respect to outstanding options held by our named executive officers at December 31, 2013.

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Option Exercises

The following table provides information regarding the exercise of options with respect to our named executive officers during 2013. We have intentionally omitted columns regarding the vesting of restricted stock, as to date we have not issued grants of restricted stock to any of our named executive officers.

Employment Agreements and Severance Agreements with Named Executive Officers

Marc Beer. In August 2010, we entered into an employment agreement with Mr. Beer for the position of Chief Executive Officer. Mr. Beer’s employment agreement provided that he would receive a specified base salary and a merit bonus of a defined percentage of his base salary. Effective January 1, 2014, Mr. Beer’s base salary, which is reviewed annually and is subject to increase but not decrease, was increased to $635,000 per year. Mr. Beer is also eligible for an annual merit bonus of up to 70% of his base salary, payable at the discretion of our Board of Directors or the Compensation Committee. Mr. Beer’s employment agreement provided for him to receive a stock option award to purchase a fixed number of shares of common stock representing approximately 6.5% of the total number of shares of our outstanding capital stock, on an as-converted basis, anticipated to be outstanding immediately prior to our initial public offering. For purposes of determining the shares subject to this stock option award, certain estimates and assumptions were mutually agreed upon by us and Mr. Beer. Mr. Beer is eligible to participate in our employee benefit plans to the extent he is eligible for those plans, on the same terms as similarly-situated executive officers of the Company.

Mr. Beer’s employment agreement also provides that, subject to nomination, election and removal procedures, he will serve on our Board of Directors for as long as he is our Chief Executive Officer.

If Mr. Beer terminates his employment for good reason (as defined in his employment agreement) or if we terminate his employment without cause (as defined in his employment agreement), he is entitled to receive as severance compensation 12 months’ base salary continuation, which will be reduced by any compensation that Mr. Beer receives from another employer within 12 months of his separation, continuation of health benefits with the Company continuing to pay its portion of the premiums for the earlier of the date that is 12 months after the date on which his employment terminates and the date he becomes re-employed with substantially comparable benefits and 25% acceleration of any unvested equity incentive awards. These payments and benefits are conditioned upon his execution of a separation agreement that includes a general release within 35 days of his termination and his compliance with certain restrictive covenants, including non-competition, non-solicitation, and confidentiality covenants.

If within 18 months of a change in control (as defined in his employment agreement), Mr. Beer’s employment is terminated without cause or he terminates his employment for good reason, he will be entitled to

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a severance payment of (1) 1.5 times the sum of his base salary plus his bonus payment for the prior year, (2) continuation of health benefits with the Company continuing to pay its portion of the premiums until the earlier of the date that is 18 months after the date on which his employment terminates and the date he becomes re-employed with substantially comparable benefits, and (3) 100% acceleration of any unvested equity incentive awards.

Mark Fitzpatrick. In May 2011, we entered into an employment agreement with Mr. Fitzpatrick for the position of Chief Financial Officer. Mr. Fitzpatrick’s employment agreement provided that he would receive a specified base salary and merit bonus of a defined percentage of his base salary. Effective January 1, 2014, Mr. Fitzpatrick’s base salary, which is reviewed annually, was increased to $370,500 per year. Mr. Fitzpatrick is also eligible for an annual merit bonus of up to 45% of his base salary, with the actual amount of any such bonus determined by the Compensation Committee and Chief Executive Officer at their discretion based upon corporate performance, Mr. Fitzpatrick’s achievement of a series of performance milestones and such other factors as the Compensation Committee, in its discretion, may deem appropriate. Mr. Fitzpatrick’s employment agreement also provided for the payment to him of a one-time signing bonus of $25,000, subject to repayment provisions that have lapsed.

Under his employment agreement, Mr. Fitzpatrick received a stock option award to purchase 220,000 shares of common stock, with 132,000 of such shares to vest in equal monthly installments over a four-year period commencing immediately after the grant date, and 88,000 of such shares to vest in equal monthly installments over a four-year period that commenced upon the date of marketing approval for JUXTAPID by the FDA. Mr. Fitzpatrick is eligible to participate in our employee benefit plans to the extent he is eligible for those plans, on the same terms as similarly situated employees of the Company.

If Mr. Fitzpatrick terminates his employment for good reason (as defined in his employment agreement) or if we terminate his employment without cause (as defined in his employment agreement), he will be entitled to receive as severance compensation 12 months’ base salary continuation, which will be reduced dollar for dollar by any compensation that Mr. Fitzpatrick receives from another employer within 12 months of his separation, and continuation of health benefits with the Company continuing to pay its portion of the premiums for the earlier of the date that is 12 months after the date on which his employment terminates and the date he becomes re-employed and eligible for health and/or dental insurance. These payments and benefits are conditioned upon his execution of a separation agreement that includes a general release of claims in a form acceptable to the Company and his compliance with certain restrictive covenants, including non-competition, non-solicitation and confidentiality covenants.

If, within 18 months of a sale event (as defined in the 2010 Option Plan), Mr. Fitzpatrick’s employment terminated without cause or he terminates his employment for good reason, in addition to the severance benefits described in the preceding paragraph, he will be entitled to receive 100% acceleration of any unvested equity incentive awards.

Martha Carter. In February 2011, we entered into an employment agreement with Ms. Carter for the position of Chief Regulatory Officer and Senior Vice President. Ms. Carter’s employment agreement provided that she would receive a specified base salary and merit bonus of a defined percentage of her base salary. Effective January 1, 2014, Ms. Carter’s base salary, which is reviewed annually, was increased to $340,000 per year. Ms. Carter is also eligible for an annual merit bonus of up to 30% of her base salary, with the actual amount of any such bonus determined by our Board of Directors and Chief Executive Officer at their discretion based upon corporate performance, Ms. Carter’s achievement of a series of performance milestones, and such other factors as our Board of Directors, in its discretion, may deem appropriate. Ms. Carter’s employment agreement also provided for the payment to her of cash milestone bonus payments equal to 5% of her base salary upon the occurrence of each of the following milestone events: (i) approval of lomitapide by the FDA, and (ii) approval of lomitapide by the EMA (collectively, the “Milestone Bonus Payments”). The Milestone Bonus Payments have been paid to Ms. Carter.

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Under her employment agreement, Ms. Carter received a stock option award to purchase 132,000 shares of common stock, with 88,000 of such shares to vest in equal monthly installments over a four-year period commencing immediately after the grant date, and 44,000 of such shares to vest in equal monthly installments over a four-year period commencing upon submission of the New Drug Application, or NDA, and Marketing Authorization Application, MAA, for lomitapide to the FDA and EMA, respectively. Ms. Carter is eligible to participate in our employee benefit plans to the extent she is eligible for those plans, on the same terms as similarly situated employees of the Company.

If Ms. Carter terminates her employment for good reason (as defined in her employment agreement) or if we terminate her employment without cause (as defined in her employment agreement), she will be entitled to receive as severance compensation 12 months’ base salary continuation, which will be reduced dollar for dollar by any compensation that Ms. Carter receives from another employer within 12 months of her separation, and continuation of health benefits with the Company continuing to pay its portion of the premiums for the earlier of the date that is 12 months after the date on which her employment terminates and the date she becomes re-employed and eligible for health and/or dental insurance. These payments and benefits are conditioned upon her execution of a separation agreement that includes a general release of claims in a form acceptable to the Company and her compliance with certain restrictive covenants, including non-competition, non-solicitation and confidentiality covenants.

If, within 18 months of a sale event (as defined in the 2010 Option Plan), Ms. Carter’s employment is terminated without cause or she terminates her employment for good reason, in addition to the severance benefits described in the preceding paragraph, she will be entitled to receive 100% acceleration of any unvested equity incentive awards

Craig Fraser. In November 2011, we entered into an employment agreement with Mr. Fraser for the position of President, U.S. Mr. Fraser was promoted to President, U.S. Commercial & Global Manufacturing and Supply Chain, in September 2012. Mr. Fraser’s employment agreement provided that he would receive a specified base salary and merit bonus of a defined percentage of his base salary. Effective January 1, 2014, Mr. Fraser’s base salary, which is reviewed annually, was increased to $365,000 per year. Mr. Fraser is also eligible for an annual merit bonus of up to 45% of his base salary, with the actual amount of any such bonus determined by our Board of Directors and Chief Executive Officer at their discretion based upon corporate performance, Mr. Fraser’s achievement of a series of performance milestones and such other factors as our Board of Directors, in its discretion, may deem appropriate. Mr. Fraser’s employment agreement also provided for the payment to him of a one-time signing bonus of $60,000, which was subject to repayment provisions that have lapsed.

Under his employment agreement, Mr. Fraser received a stock option award to purchase 100,000 shares of common stock, with such shares to vest in equal monthly installments over a four-year period commencing immediately after the grant date. Mr. Fraser is eligible to participate in our employee benefit plans to the extent she is eligible for those plans, on the same terms as similarly situated employees of the Company.

If Mr. Fraser terminates his employment for good reason (as defined in his employment agreement) or if we terminate his employment without cause (as defined in his employment agreement), he will be entitled to receive as severance compensation 6 months’ base salary continuation, which will be reduced dollar for dollar by any compensation that Mr. Fraser receives from another employer within 6 months of his separation, and continuation of health benefits with the Company continuing to pay its portion of the premiums for the earlier of the date that is 6 months after the date on which his employment terminates and the date he becomes re-employed and eligible for health and/or dental insurance. These payments and benefits are conditioned upon his execution of a separation agreement that includes a general release of claims in a form acceptable to the Company and his compliance with certain restrictive covenants, including non-competition, non-solicitation and confidentiality covenants.

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If, within 18 months of a sale event (as defined in the 2010 Option Plan), Mr. Fraser’s employment is terminated without cause or he terminates his employment for good reason, in addition to the severance benefits described in the preceding paragraph, he will be entitled to receive 100% acceleration of any unvested equity incentive awards.

Mark Sumeray. In August 2011, we entered into an employment agreement with Dr. Sumeray for the position of Chief Medical Officer. Dr. Sumeray’s employment agreement provided that he would receive a specified base salary and merit bonus of a defined percentage of his base salary. Effective January 1, 2014, Dr. Sumeray’s base salary was $405,000 per year and Dr. Sumeray is also eligible for a merit bonus of up to 45% of his base salary, with the actual amount of any such bonus determined by our Board of Directors and Chief Executive Officer at their discretion based upon corporate performance, Dr. Sumeray’s achievement of a series of performance milestones and such as other factors as our Board of Directors, in its discretion, may deem appropriate. Dr. Sumeray’s employment agreement also provided for the payment to him of a one-time signing bonus of $60,000, which was subject to repayment provisions that have lapsed.

Under his employment agreement, Dr. Sumeray received, until December 31, 2013, a housing allowance of up to $3,675 per month for an apartment in the Cambridge, Massachusetts area, which allowance was subject to assessment by us from time to time at our discretion. This housing allowance was eligible to be grossed up to a maximum of $5,145 per month to help offset a portion of Dr. Sumeray’s tax liabilities relating to such housing allowance. We also agreed to reimburse Dr. Sumeray’s travel expenses directly related to his commuting to the Cambridge, Massachusetts area, which reimbursements are also eligible to be grossed up to a maximum of 40% of the aggregate amount of such expenses, on a quarterly basis, to help offset Dr. Sumeray’s tax liabilities associated with such travel reimbursements. We agreed to provide these benefits through December 31, 2013 and, after that, to cover reasonable expenses related to his relocation to Cambridge.

Under his employment agreement, Dr. Sumeray received a stock option award to purchase 180,000 shares of our common stock under the 2010 Option Plan, with 100,000 of such shares to commence vesting upon the grant date and 80,000 of such shares to commence vesting in four tranches commencing upon the achievement of specific milestones. As approved by our Board of Directors, the options to purchase 100,000 of such shares commenced vesting in installments over a 46-month period, with 1/24 of such shares vesting on the grant date and the remainder of the shares vesting in 46 equal monthly installments over the 46-month period commencing immediately after the grant date, and the options to purchase 80,000 of such shares to vest upon the achievement of certain performance objectives, as set forth in Footnote 7 to the “Outstanding Equity Awards at Year-End” table in this proxy statement.

If Dr. Sumeray terminates his employment for good reason (as defined in his employment agreement) or if we terminate his employment without cause (as defined in his employment agreement), he is entitled to receive as severance compensation 12 months’ base salary continuation, which will be reduced dollar for dollar by any compensation that Dr. Sumeray receives from another employer within 12 months of his separation, and continuation of health benefits with the Company continuing to pay its portion of the premiums for the earlier of the date that is 12 months after the date on which his employment terminates and the date he becomes re-employed and eligible for health and/or dental insurance. These payments and benefits are conditioned upon his execution of a separation agreement that includes a general release of claims in a form acceptable to the Company and his compliance with certain restrictive covenants, including non-competition, non-solicitation and confidentiality covenants.

If, within 18 months of a sale event (as defined in the 2010 Option Plan), Dr. Sumeray is terminated without cause or he terminates his employment for good reason, in addition to the severance benefits described in the preceding paragraph, he will be entitled to 100% acceleration of any unvested equity incentive awards.

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Potential Payments Upon Termination or Change-in-Control

The table below reflects, as applicable, cash severance, option acceleration, continuation of health benefits, and accrued vacation benefits payable to our named executive officers (1) in connection with the termination of his or her employment relationship without cause or resignation for good reason and (2) in connection with termination without cause or resignation for good reason following a sale event or a change in control, as applicable, in each case, and assuming that the triggering event took place on December 31, 2013. See also “—Employment Agreements and Severance Agreements with Executive Officers.”

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The 2010 Option Plan provides that upon the effective time of a “sale event” (as defined below), except as otherwise provided in an award agreement, all awards under the 2010 Option Plan will automatically terminate, unless the parties to the sale event agree that such awards will be assumed or continued by the successor entity. In the event of such termination, all options and stock appreciation rights will become fully exercisable as of the effective time of the sale event and all other awards will become fully vested and nonforfeitable as of the effective time of the sale event, except as the administrator may otherwise specify with respect to particular awards, and any awards with conditions and restrictions relating to the attainment of performance goals may become vested and nonforfeitable in connection with a sale event in the administrator’s discretion. In the event of such termination, participants holding options and stock appreciation rights will be permitted to exercise such options and stock appreciation rights prior to the sale event. In addition, in the case of a sale event in which our stockholders will receive cash consideration, we may make or provide for a cash payment to participants holding options and stock appreciation rights equal to the difference between the per share cash consideration and the exercise price of the options or stock appreciation rights. Under the 2010 Option Plan, a sale event is defined as the consummation of:

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SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

Section 16(a) of the Exchange Act requires our executive officers, directors and persons holding more than 10% of our common stock to file initial reports of beneficial ownership and changes in beneficial ownership of our securities. Based solely on information provided to us by our directors and executive officers, we believe that, during 2013, all such parties timely filed all reports they were required to file under Section 16(a).

EQUITY COMPENSATION PLANS

The following table provides information as of December 31, 2013 relating to our equity compensation plans:

CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

Since January 1, 2013, we have not engaged in any “related person” transactions with our directors, executive officers or holders of 5% or more of our voting securities, affiliates or any member of the immediate family of the foregoing persons.

Policies for Approval of Related Person Transactions

Our Board of Directors reviews and approves any transaction between the Company and any director, officer or holder of 5% or more of our voting securities, or their respective affiliates, each, a related person. We have adopted a related person transaction approval policy that governs the review of related person transactions. Pursuant to this policy, if we want to enter into a transaction with a related person, our general counsel will review the proposed transaction to determine, based on applicable NASDAQ Rules and SEC rules, if such transaction requires pre-approval by the Audit Committee and/or Board of Directors. If pre-approval is required, such matters will be reviewed at the next regular or special Audit Committee and/or Board of Directors meeting. We may not enter into a related person transaction unless our general counsel has either specifically confirmed in writing that no further reviews are necessary or that all requisite corporate approvals have been obtained.

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PROPOSAL NO. 1 – ELECTION OF DIRECTORS

Our Board of Directors has voted to nominate Dr. Sol Barer and Dr. Antonio Gotto for election as Class I directors at the Annual Meeting, each to serve for a term of three years until the 2017 Annual Meeting of Stockholders and until their respective successors are duly elected and qualified.

Unless authority to vote for any of these nominees is withheld, the shares represented by the enclosed proxy will be voted FOR the election of Dr. Sol Barer and Dr. Antonio Gotto as Class I directors. In the event that either nominee becomes unable or unwilling to serve, the shares represented by the enclosed proxy will be voted for the election of such other person as our Board of Directors may recommend in his or her place. We have no reason to believe that either nominee will be unable or unwilling to serve as a director.

A plurality of the shares voted at the Annual Meeting is required to elect each nominee as a director.

Our Board of Directors recommends a vote “FOR” the election of each of Dr. Sol Barer and Dr. Antonio Gotto as a Class I director, and proxies solicited by the Company will be voted in favor thereof unless a stockholder has indicated otherwise on the proxy.

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PROPOSAL NO. 2 – ADVISORY VOTE ON EXECUTIVE COMPENSATION

Section 14A of the Securities Exchange Act of 1934 requires that we provide our stockholders with the opportunity to vote to approve, on a non-binding, advisory basis, the compensation of our named executive officers. The vote on Proposal No. 2 is not intended to address a specific element of compensation. Instead, the vote relates to the compensation of our named executive officers, as described in this proxy statement.

Our Board of Directors is asking stockholders to support this Proposal No. 2 by casting a non-binding, advisory vote “FOR” the compensation paid to our named executive officers in 2013, based on the disclosure set forth in this proxy statement pursuant to the compensation disclosure rules of Item 402 of Regulation S-K, including the Compensation Discussion and Analysis section, compensation tables, and related narrative discussion, which, among other things, demonstrates our:

Although the say-on-pay vote we are asking you to cast is non-binding, our Board of Directors and the Compensation Committee value the views of our stockholders and will consider the outcome of the vote when determining future compensation arrangements for our named executive officers.

Approval of the advisory vote on the compensation of our named executive officers requires that the holders of a majority of the shares present in person or represented by proxy and entitled to vote at the Annual Meeting vote “FOR” this Proposal No. 2. This vote is non-binding. We currently hold our say-on-pay vote every three years. The next advisory vote on the compensation of our named executive officers will occur no later than 2017.

Our Board of Directors recommends a vote “FOR” the advisory vote to approve the compensation of our named executive officers.

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PROPOSAL NO. 3 – RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Audit Committee has directed the Company to submit the selection of Ernst & Young LLP as the Company’s independent registered public accounting firm for 2014 for ratification by the stockholders at the Annual Meeting. Neither our by-laws nor our other governing documents or law require stockholder ratification of the selection of Ernst & Young LLP as the Company’s independent registered public accounting firm. However, the Audit Committee is submitting the selection of Ernst & Young LLP to the stockholders for ratification as a matter of good corporate practice. If the stockholders fail to ratify the selection, the Audit Committee will reconsider whether or not to retain that firm. Even if the selection is ratified, the Audit Committee may, in its discretion, direct the appointment of a different independent registered public accounting firm at any time during 2014 if it determines that such a change would be in the best interests of the Company and its stockholders.

A representative of Ernst & Young LLP is expected to attend the Annual Meeting and will have the opportunity to make a statement if he or she so desires, and will be available to respond to appropriate questions of stockholders.

Ratification of the selection of Ernst & Young LLP requires that the holders of a majority of the shares present in person or represented by proxy and entitled to vote at the Annual Meeting vote “For” this Proposal No. 3. An abstention vote will have the same effect as a vote “Against” this Proposal No. 3. Discretionary votes by banks, brokers and other nominees on this routine proposal will be counted towards the quorum requirement and will affect the outcome of the vote.

Our Board of Directors recommends a vote “FOR” the ratification of the appointment of Ernst & Young LLP as our independent registered public accounting firm for 2014.

Report of the Audit Committee

The Audit Committee has reviewed and discussed our audited financial statements with management. In addition, the Audit Committee has discussed with Ernst & Young LLP, our independent registered public accounting firm, the matters required to be discussed by the Statement on Auditing Standards No. 61, as amended, as adopted by the Public Accounting Oversight Board in Rule 3200T, which includes, among other items, matters related to the conduct of the audit and our financial statements. The Audit Committee has also reviewed the written disclosures and letter required by applicable requirements of the Public Company Accounting Oversight Board regarding Ernst & Young LLP’s communications with the Audit Committee concerning independence. The Audit Committee has reviewed with Ernst & Young LLP its independence from the Company.

Based on the Audit Committee’s review of the audited financial statements and discussions with management and Ernst & Young LLP, the Audit Committee unanimously recommended to our Board of Directors that the audited financial statements be included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2013, for filing with the SEC.

By the Audit Committee of the Board of Directors of Aegerion Pharmaceuticals, Inc.

Anne VanLent, Chair of the Audit Committee

Paul G. Thomas

Sandford D. Smith

This report shall not constitute “soliciting material,” shall not be deemed “filed” with the SEC and is not to be incorporated by reference into any of our other filings under the Securities Act or the Exchange Act, except to the extent that we specifically incorporate this report by reference therein.

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Fees and Services of Ernst & Young LLP

The following sets forth fees billed for audit and other services provided by Ernst & Young LLP for the fiscal years ended December 31, 2013 and December 31, 2012:

The Audit Committee has adopted a Pre-Approval Policy for Audit and Non-Audit Service, or the Pre-Approval Policy, which sets forth the procedures and the conditions pursuant to which services to be performed by the independent registered accounting firm may be pre-approved. Unless a type of service has been pre-approved pursuant to the Pre-Approval Policy, it must be separately pre-approved by the Audit Committee or the Chair of the Audit Committee before it may be provided by the independent registered accounting firm. Pursuant to the Pre-Approval Policy, certain audit services, audit-related services, tax services and other services have been pre-approved by the Audit Committee. Below is a brief summary of each category of services and the types of services that the Audit Committee has pre-approved in such category.

Audit services are services necessary for the audit of our annual financial statements and the review of our quarterly financial statements and services that are normally provided by the accountants in connection with statutory and regulatory filings or engagements.

Audit-related services are assurance and related services that are reasonably related to the performance of the audit or review of our financial statements that are traditionally performed by the independent auditor.

Tax services are professional services rendered for tax compliance, tax advice and tax planning. Services include tax services related to U.S. federal, state and local tax planning and advice and compliance, international tax planning and compliance, review of federal, state, local and international income, franchise and other tax reports and licensing or purchase of income tax preparation software from the independent registered accounting firm, provided the functionality is limited to preparation of tax returns.

Other services are services other than audit, audit-related or tax services that are routine and recurring services that would not impair the independence of the auditor.

All of the services performed by the independent registered accounting firm that were performed in our fiscal years ended December 31, 2013 and December 31, 2012 were pre-approved by the Audit Committee.

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STOCKHOLDER PROPOSALS

In order to be considered for inclusion in the Company’s proxy materials for the 2015 Annual Meeting of Stockholders pursuant to Rule 14a-8 under the Exchange Act, stockholders’ proposals must be received by us at our principal executive offices at 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142 no later than December 31, 2014. Proposals received after that date will not be considered for inclusion in the Company’s proxy materials for the 2015 annual meeting.

Stockholders who intend to present a proposal or nominate a director at the 2015 Annual Meeting of Stockholders without inclusion in our proxy materials pursuant to Rule 14a-8 under the Exchange Act are required to provide advance written notice of such proposal to us, at the address listed in the following paragraph, not earlier than February 25, 2015 and not later than March 27, 2015; provided, however, that in the event that the date of the 2015 Annual Meeting of Stockholders is more than thirty (30) days before or more than sixty (60) days after the anniversary date of this year’s annual meeting of stockholders, or if no annual meeting of stockholders were held for 2014, notice by the stockholder to be timely must be delivered not earlier than the close of business on the ninetieth (90th) day prior to the 2015 Annual Meeting of Stockholders and not later than the close of business on the later of the sixtieth (60th) day prior to the 2015 Annual Meeting of Stockholders or the tenth (10th) day following the day on which we first make a public announcement of the date of the 2015 Annual Meeting of Stockholders.

All stockholder proposals should be delivered to the attention of our Secretary, c/o Aegerion Pharmaceuticals, Inc., 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142. We suggest that proposing stockholders submit his or her proposals by certified mail, return receipt requested. We advise you to review our Amended and Restated By-laws, which contain additional requirements about advance notice of stockholder proposals and director nominations. If a proposal is received on a timely basis and properly comes before the meeting, management may still exercise discretionary voting authority on the proposal in connection with proxies solicited by the Company for the meeting under circumstances consistent with the proxy rules of the SEC.

HOUSEHOLDING OF MEETING MATERIALS

We have adopted a procedure approved by the SEC called “householding.” Under this procedure, beneficial owners of our common stock who have the same address and last name and have not previously requested electronic delivery of proxy materials will receive a single envelope containing the Notice for all beneficial owners of our common stock having that address. This procedure will reduce our printing costs and postage fees. If, in the future, you do not wish to participate in householding and prefer to receive your Notice in a separate envelope, please contact the Investor Relations Department at 101 Main Street, Suite 1850, Cambridge, Massachusetts 02142, or e-mail Investor Relations at investorrelations@aegerion.com. We will respond promptly to such requests.

For those beneficial owners who have the same address and last name and who request to receive a printed copy of the proxy materials by mail, we will send only one copy of such materials to each address unless one or more of those beneficial owners notifies us, in the same manner described above, that they wish to receive a printed copy for each beneficial owners at that address.

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GENERAL

Management does not intend to bring any business before the Annual Meeting other than the matters referred to in the accompanying notice. If, however, any other matters properly come before the Annual Meeting, it is intended that the persons named in the accompanying proxy will vote pursuant to the proxy in accordance with their best judgment on such matters.

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		REVOCABLE PROXY AEGERION PHARMACEUTICALS, INC.

FOLD HERE IF YOU ARE VOTING BY MAIL

PLEASE DO NOT DETACH

The Board of Directors recommends a vote “FOR” the nominees.

AEGERION PHARMACEUTICALS, INC. – ANNUAL MEETING, JUNE 25, 2014

YOUR VOTE IS IMPORTANT!

Annual Meeting Materials are available on-line at:

http://www.rrdezproxy.com/2014/Aegerion

You can vote in one of three ways:

or

or

PLEASE SEE REVERSE SIDE FOR VOTING INSTRUCTIONS

(Continued, and to be marked, dated and signed, on the other side)

REVOCABLE PROXY

AEGERION PHARMACEUTICALS, INC.

ANNUAL MEETING OF STOCKHOLDERS

June 25, 2014

9:00 a.m. (EDT)

THIS PROXY IS SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS

The undersigned hereby makes, constitutes and appoints Mark J. Fitzpatrick and Anne Marie Cook, or either one of them, attorneys and proxies, with power of substitution in each, to act for the undersigned with respect to all shares of Common Stock of Aegerion Pharmaceuticals, Inc. held of record by the undersigned on April 28, 2014, at the Annual Meeting of Stockholders to be held at One Main Street, East Arcade Conference Center, Cambridge, MA 02142, on Wednesday, June 25, 2014, at 9:00 a.m. (EDT), or any adjournment or postponement thereof, for the following purposes:

THIS PROXY WHEN PROPERLY EXECUTED WILL BE VOTED IN THE MANNER DIRECTED HEREIN BY THE STOCKHOLDER. IF NO DIRECTION IS MADE, THIS PROXY WILL BE VOTED FOR THE NOMINEES LISTED IN ITEM 1 AND FOR ITEM 2 AND ITEM 3.

PLEASE PROVIDE YOUR INSTRUCTIONS TO VOTE BY TELEPHONE OR THE INTERNET OR

COMPLETE, DATE, SIGN, AND MAIL THIS PROXY CARD PROMPTLY

IN THE ENCLOSED POSTAGE-PAID ENVELOPE.