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):

May 7, 2013

Dear Stockholder:

We are pleased to invite you to attend our 2013 Annual Meeting of Stockholders, or the Annual Meeting. The Annual Meeting will be held on Wednesday, June 26, 2013, 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 29, 2013, 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 29, 2013 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 2013 ANNUAL MEETING OF STOCKHOLDERS

To our Stockholders:

The 2013 Annual Meeting of Stockholders of Aegerion Pharmaceuticals, Inc., or the Annual Meeting, will be held on Wednesday, June 26, 2013, 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 29, 2013. 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 2012 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, 2013, 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: May 7, 2013

AEGERION PHARMACEUTICALS, INC.

101 Main Street

Suite 1850

Cambridge, Massachusetts 02142

www.aegerion.com

PROXY STATEMENT—2013 ANNUAL MEETING OF STOCKHOLDERS

This proxy statement contains information about the 2013 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 26, 2013, 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 29, 2013, the record date, are entitled to vote at the Annual Meeting. On the record date, there were 28,817,714 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 not in your name, but rather 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, 2013, 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, 2013, we will begin mailing a Notice Regarding Internet Availability of Proxy Materials, or the Proxy Notice, to all stockholders who held shares in street name. We have posted our proxy materials on the website referenced in the Proxy Notice (www.proxyvote.com). You may choose to access our proxy materials on the website referenced in the Proxy 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, 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.

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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 2013 (Proposal No. 2) is considered routine under applicable rules. The election of directors (Proposal No. 1) is 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 a plurality of the votes of the shares of our common stock present in person or represented by proxy at the Annual Meeting and entitled to vote.

Proposal No. 2 – 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 2013. 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 2013 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 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.

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 within four business days after the Annual Meeting.

Attending the Annual Meeting

The Annual Meeting will be held on Wednesday, June 26, 2013 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, 2013 (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, 2013, 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 28,811,589 shares of common stock outstanding on April 15, 2013.

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 Mr. Beer and Mr. Scheer for re-election as Class III directors at the Annual Meeting, for a term of three years, to serve until the 2016 Annual Meeting of Stockholders and until their respective successors have been duly elected and qualified. Our Board of Directors has determined that Mr. Beer and Mr. Scheer 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

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.

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David I. Scheer, a co-founder of the Company, has served as Chairman of our Board of Directors since 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 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. 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.

Directors Whose Terms Do Not Expire This Year

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 commercialization of stent system technology), Medgenics (a gene therapy company) 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 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.

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

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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 Board of Trustees 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, and since September 2009 has served as Chief Executive Officer, 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). 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 director and chair of the audit committee for Tranzyme Pharma, Inc., a NASDAQ-listed company, and as a director of Integra Life Sciences, where she served as chair of the audit committee from 2005 to 2012. During the past five years, Ms. VanLent also served as a director of Penwest Pharmaceuticals Co., until its sale to Endo Pharmaceuticals in the fall of 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.

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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. In making the determinations of independence, our Board of Directors took into consideration the consulting services that Dr. Gotto provided to us in connection with our preparations for the meeting of the Endocrinologic and Metabolic Drugs Advisory Committee, or EMDAC, of the U.S. Food and Drug Administration, or FDA, in October 2012 at which our product, JUXTAPID™ (lomitapide) capsules, or JUXTAPID, was reviewed by EMDAC as a potential treatment for homozygous familial hypercholesterolemia, or HoFH. For such services, we paid Dr. Gotto a total of $19,500 in consulting fees in 2012. 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 seven meetings in 2012.

The following table provides information about the membership and meetings of the standing committees of our Board of Directors in 2012.

All of the members of these committees served on the applicable committees for all of 2012, except for Mr. Scheer, who was appointed to the Audit Committee in May 2012. During 2012, each director attended at least 75% of the meetings of our Board of Directors and the committees on which he served. In connection with the appointment of Ms. VanLent to the Board of Directors in April 2013, Ms. VanLent was appointed Chair of the Audit Committee and Mr. Scheer stepped down from the Audit Committee.

The independent directors meet in executive session without management directors or management present. These sessions take place prior to or following regularly scheduled Board of Directors and most scheduled committee meetings. The independent directors met in executive session after each Board of Directors meeting held during 2012.

Annual Stockholder Meetings

Our policy has been 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 2012, Mr. Beer and Mr. Smith attended our annual meeting of stockholders.

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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 are intended to 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.

Code of Conduct and Ethics

Our Board of Directors has adopted a code of business conduct and ethics 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.

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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 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 our 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 the Compensation Committee. None of the members of the 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 and 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. 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:

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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. After reviewing benchmarking information from the same companies included in our 2012 peer group for executive compensation and other information provided by Radford Consulting, an Aon Hewitt Company, or Radford, independent consultant to the Compensation Committee, our Board of Directors, based, in part, upon the recommendation of the Compensation Committee, amended the cash compensation policy in December 2012. The amended policy took effect on January 1, 2013.

Cash Compensation

Below is a summary of cash compensation payable to non-employee directors in 2012 and 2013:

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

Equity Awards

Prior to amendment of the policy in December 2012, each person who was initially appointed or elected to our Board of Directors was eligible for an option grant to purchase shares of common stock, representing 0.1% of shares of our common stock on a fully-diluted basis on the date he or she first became a non-employee director. In addition, each director was entitled to an annual option grant to purchase shares of common stock representing 0.05% of the shares of our common stock on a fully-diluted basis as of the date of our annual stockholders meeting. So long as the director remains on our Board of Directors, each option granted prior to December 2012 vests in equal one-third installments on the anniversary of the date of grant, beginning on the first anniversary of the date of grant.

In addition, prior to amendment of the policy in December 2012, the Chairman of the Audit Committee and the Chairman of the Compensation Committee were each entitled to receive a one-time grant of restricted stock equal to 0.15% of shares of our common stock on a fully-diluted basis when they were first elected to such position. These restricted stock grants vest in the same manner as the director option grants described above. Beginning in 2013, under the amended policy, we will not make separate equity awards to the Chairs of these committees upon appointment.

Based on amendments to the Non-Employee Director Compensation Policy approved by the Board in December 2012, as further amended in April 2013, each person who is initially appointed or elected to the Board of Directors in 2013 will be eligible to receive an option grant to purchase 14,700 shares of common stock. As a result, Ms. VanLent received an option to purchase 14,700 shares upon her appointment to the Board of Directors on April 26, 2013. In addition, on the date of the Annual Meeting, each director, except for Ms. VanLent, will be eligible to receive an annual option grant to purchase 14,700 shares of common stock. So long as the director remains on the Board of Directors, 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.

Under the amended Non-Employee Director Compensation Policy, the size of the initial grant for 2014 and any subsequent year shall be determined in December of the preceding year, and shall equal $370,000 divided by a Black-Scholes-adjusted 30 day average stock price. The size of the annual grant for 2014 and any subsequent year shall similarly be determined in December of the preceding year, and shall equal $185,000 divided by the Black-Scholes-adjusted 30 day average.

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. In addition, for options granted in 2012, directors will have up to 12 months following cessation of service as a director to exercise the options (to the extent vested at the date of such cessation), provided that the director has not been removed for cause. For options granted in 2013, directors will have up to three years following cessation of service as a director to exercise the 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 at fair market value on the date of grant.

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Director Compensation Table

The following table sets forth a summary of the compensation earned by our non-employee directors in 2012. Ms. VanLent was appointed to the Board of Directors in April 2013. As a result, she did not receive any compensation from us in 2012. We have intentionally omitted columns from this table pertaining to types of compensation not paid to our non-employee directors in 2012.

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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, 2013:

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 for 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 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 medicine 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 our compensation programs, the decisions we made in 2012 under those programs with respect to our named executive officers, and the factors we considered in making those decisions. We also address the compensation programs we have implemented in 2013 for our current named executive officers. This background 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 context as we describe our overall compensation program.

Our “named executive officers” for 2012 are:

We have also included a former employee, Mark Rothera, as a named executive officer for 2012. Mr. Rothera served as our Global President from April 2012 to September 2012, and left the company in January 2013.

Executive Summary

General

Our overall compensation objectives are to attract, retain, and motivate executives who possess the leadership skills and experience necessary for our corporate success. Our compensation programs are also designed to drive and reward performance of our executives against short-term and long-term goals that align with annual operating objectives and the interests of our shareholders in building long-term value. We believe this is accomplished through the following principles and processes that we follow in establishing executive compensation:

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Overview of Our Executive Compensation Objectives and Philosophy

Our overall compensation objectives are to attract, retain, and motivate executives who possess the leadership skills and experience necessary for our corporate success. Our compensation programs are also designed to drive and reward performance of our executives against short-term and long-term goals that align with annual operating objectives and the long-term interests of our shareholders. We apply a “pay for performance” philosophy to align the incentives of our executives with the creation of stockholder value.

Specifically our compensation programs are designed to:

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To achieve these objectives, we seek to provide a competitive total compensation package that aligns a substantial portion of the executive’s overall compensation to both our corporate goals and the executive’s individual performance. As noted above, all of the critical elements of our compensation and our compensation decisions take into account the data on our peer group and the data on similarly-situated companies provided in the Radford Global Life Sciences Survey. In addition to such data, base salary increases are also determined based on an assessment of the executive’s individual performance and contribution to our corporate achievements. Annual bonus payments are determined based on a number of factors in addition to benchmarking data, including the executive’s target bonus percentage, and actual corporate and individual performance against goals. Equity awards are used to promote employee retention, and to align incentives with the creation of long-term stockholder value. The size of equity awards for our executives is determined based on each individual’s contribution to our overall corporate achievement, in addition to benchmarking data. All compensation decisions are assessed within the framework of our financial position and general economic conditions.

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 our Chief Executive Officer. Since 2011, the Compensation Committee has engaged Radford 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 2012, Radford assisted in analysis of competitive market data. Data sources included public company proxy statements and third-party industry compensation surveys. 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 peers in 2012 at the 50^th percentile, and in 2013 at the 50^th to 75^th percentile in order to enable us to attract and retain top talent.

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On an annual basis, Radford recommends, and the Compensation Committee approves, a group of comparable companies as our peer group. Our peer group for 2012 compensation was approved by the Compensation Committee in October 2011 and our peer group for 2013 compensation was approved by the Compensation Committee in October 2012. Each of these peer groups is listed in the table below. The primary reason for the changes to the peer group from 2012 to 2013 was the evolution of our business profile, and the need to adjust the peer group to include comparable companies with commercial products and with market capitalizations closer to our average market capitalization at the time of the 2013 peer group selection. Each of the peer groups was 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 2012 peer group was used to establish the 2012 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. The 2013 peer group was used to establish, among other things, the elements of 2013 compensation described in this Compensation Discussion and Analysis section.

2012 Performance Highlights

2012 was a significant year for the Company and built on our significant accomplishments in 2011, as described below. In 2012, we had a number of major accomplishments, including the following:

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2011 Performance Highlights

Our accomplishments in 2011 included:

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 earned by our named executive officers in 2012.

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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 executives’ overall compensation to the achievement of both short- and long-term corporate goals and key performance milestones.

2012 Compensation

Our 2012 compensation decisions reflect the performance of our named executive officers in achieving our performance goals, including those set forth above under “2012 Performance Highlights” and “2011 Performance Highlights.”

Base Salary

Base salary for our named executive officers provides the fixed cash component of an executive’s compensation. The goal is to initially align base salaries generally at the 50^th 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. In determining the salary increases in 2013 for our named executive officers, we targeted salaries in the 50th percentile or higher based on experience, performance and value creation.

The base salaries of our named executive officers during 2011, 2012 and 2013 are set forth in the table below.

In 2013 and 2012, the base salaries of those named executive officers listed below were increased based on merit and, in certain instances, a market adjustment, as follows.

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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 and other employees. Each named executive officer has a target cash bonus amount that is based on a percentage of his or her base salary. The target cash bonus percentages for the named executive officers in 2012, 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

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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 bonus payments made to our named executive officers for 2012 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.

The Compensation Committee established a corporate performance score of 130% for 2012. This determination was based on the Compensation Committee’s assessment of both our level of achievement against our approved 2012 corporate performance goals, as set forth below, and the overall level of our performance, including the achievements set forth above under “2012 Performance Highlights.” The Compensation Committee awarded a level of achievement above that determined solely by the numerical assessment of achievement against our approved 2012 corporate performance goals. The Compensation Committee elected to do this based on its assessment and determination that the formulaic calculation of 2012 corporate goal achievement did not accurately reflect the significant corporate performance delivery in 2012, including the achievements set forth above under “2012 Performance Highlights,” and did not appropriately take into account the fact that some of the approved 2012 corporate goals were not achieved because of changes in overall corporate strategy.

Our approved 2012 corporate goals consisted of:

As noted above, 20% of the performance bonuses of each named executive officer, other than Mr. Beer, is measured by reference to achievement of individual performance goals. The Compensation Committee concluded that in 2012 each of these named executive officers fully met or exceeded their individual’s performance goals. The individual performance goals in 2012 for each of the named executive officers, other than Mr. Beer, are described below:

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Based on the corporate goal score of 130% and, where applicable, the level of achievement against individual goals, the Compensation Committee awarded cash bonuses for 2012 to the named executive officers, as follows:

Under Mr. Rothera’s Separation Agreement, dated as of November 5, 2012, Mr. Rothera was eligible to receive a 2012 cash bonus in an amount determined by the Compensation Committee based on the corporate goal score and Mr. Rothera’s level of achievement against individual performance goals. As noted above, 20% of his performance bonus was based on achievement of individual performance goals. The Separation Agreement provided that management would recommend that Mr. Rothera receive 100% level of achievement against individual goals if the corporate goal score was 100% or higher and the same percentage level of achievement as the corporate goal score if the corporate goal score was under 100%. As a result, Mr. Rothera received a 100% level of achievement against his 2012 individual goals and 130% level of achievement against corporate goals. In addition, under the Separation Agreement, Mr. Rothera’s 2012 bonus was prorated, such that the amount of his bonus payment was based on the period from April 2, 2012, his employment start date, and November 5, 2012. As a result, Mr. Rothera received a bonus for 2012 of $117,953.

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 focus 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 initial employment and upon promotion, as applicable, and is eligible to receive annual stock option grants in an amount commensurate with individual and corporate performance based upon an option budget and approved ranges established by the Compensation Committee. 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. These stock options are earned on the basis of continued service and generally vest over four years in equal monthly installments commencing either immediately after the date of grant or, in the case of performance-based awards, 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.

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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 annual management incentive cash bonuses 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 will be three years. The first cycle covers 2012 through 2014 and the second cycle covers 2013 through 2015. The first- and second-cycle awards consist of stock options granted at the commencement of the 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 JUXTAPID. 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 JUXTAPID.

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 executives who directly report to our Chief Executive Officer will typically be included 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. Performance-based awards, including performance-based options, will be granted and/or allocated by specific numbers or 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 executive officers, the Compensation Committee utilizes competitive market data provided by Radford for the executive’s position and a determination of the executive’s level of responsibility, and potential contribution to the advancement of our corporate objectives. Typically, larger awards have been made to the named executive officers with areas of responsibility and functions that are more likely to build long-term stockholder value as determined by how directly linked their areas of responsibility are to our growth and key milestones.

In 2012, the Compensation Committee made option grants to the named executive officers as follows:

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Equity Grant Approvals/Timing

All grants for 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 other employees based on a budget approved by the Compensation Committee and consistent with our overall compensation philosophy. All stock options will be awarded with a grant price equal to fair value 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 in Connection with Change-in-Control” for a discussion of the change-in-control provisions related to stock options.

Other Compensation

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

Our employee savings 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. We did match employee contributions in 2012. We may make matching contributions or additional contributions to our 401(k) plan in amounts determined annually.

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 provide 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 current amount of this allowance, including the cost to offset the associated tax liability, is $5,145 per month. We have 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 have agreed to provide these benefits to Dr. Sumeray through December 31, 2013 and, after that, we will cover reasonable expenses related to his relocation to Cambridge.

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Pursuant to his employment agreement, we agreed to reimburse Mr. Rothera for expenses directly related to his relocation to the Cambridge area, up to a maximum amount of $100,000. We also agreed to repay Mr. Rothera for any payments he became required to make to his former employer for relocation expenses provided to him by such employer, up to a maximum amount of $37,500. Mr. Rothera’s employment with the Company terminated in January 2013 and, under his Separation Agreement, we agreed to reimburse Mr. Rothera for a defined set of relocation and housing expenses, and to gross up such reimbursement payments to cover estimated taxes that Mr. Rothera would incur as a result of such payments.

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 in Connection with Change-in-Control,” we have agreements with our named executive officers providing certain severance benefits to them upon termination of their employment or in relation to 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 cash continuity protection such that a named executive officer will devote his or her full time and attention to the requirements of the business rather than 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 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. We expect that the Compensation Committee will continue to consider the outcome of future advisory votes on executive compensation when making future compensation decisions with respect to our named executive officers. The next such Say-on-Pay advisory vote is scheduled to be held at our annual meeting of stockholders in 2014.

Section 162(m) of the Internal Revenue Code

Section 162(m) of the Code places a limit of $1 million on the amount of compensation that a public company may deduct in any one year with respect to its chief executive officer and other named executive officers (other than its chief financial officer) unless compensation qualifies as performance-based under such section. The Compensation Committee may seek to qualify the variable compensation paid to our named executive officers for an exemption from the deductibility limitations under Section 162(m). However, the Compensation Committee may, in its judgment, authorize compensation payments that do not comply with the exemptions, in whole or in part, under Section 162(m) or that may otherwise be limited as to tax deductibility.

Accounting Considerations

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 2012.

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 2012.