SCHEDULE 14A

INFORMATION REQUIRED IN PROXY STATEMENT

SCHEDULE 14A INFORMATION

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:

SYNAGEVA BIOPHARMA CORP.

(Name of Registrant as Specified In Its Charter)

(Name of Person(s) Filing Proxy Statement, if other than the Registrant)

Payment of Filing Fee (Check the appropriate box):

Lexington, MA

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS

To Be Held On June 4, 2014

Dear Stockholder:

You are cordially invited to attend Synageva’s Annual Meeting of Stockholders (the “Annual Meeting”) on Wednesday, June 4, 2014 at 4:30 p.m., local time, at the offices of Ropes & Gray LLP, Prudential Tower, 800 Boylston Street, Boston, Massachusetts 02199. We are asking stockholders:

Stockholders of record at the close of business on April 11, 2014 will be entitled to notice of, and to vote at, the Annual Meeting or any adjournment of the Annual Meeting.

All stockholders are cordially invited to attend the Annual Meeting in person. However, whether or not you plan to attend the Annual Meeting, please vote by mail, by phone or on the Internet at your earliest convenience so that your shares may be represented at the Annual Meeting and to ensure a quorum.

Important Notice Regarding the Availability of Proxy Materials for

the Annual Meeting to be held on June 4, 2014.

This Proxy Statement and our 2013 Annual Report are available at

www.synageva.com

Sanj K. Patel

President and Chief Executive Officer

Lexington, Massachusetts

April 23, 2014

PROXY STATEMENT

GENERAL INFORMATION

Proxy Solicitation

This Proxy Statement and form of proxy are furnished to the holders of Synageva common stock, par value $0.001 per share, in connection with the solicitation by our Board of Directors of proxies for use at the Annual Meeting of Stockholders (the “Annual Meeting”) to be held on Wednesday, June 4, 2014 at 4:30 p.m., local time, at the offices of Ropes & Gray LLP, Prudential Tower, 800 Boylston Street, Boston, Massachusetts 02199, or at any adjournment thereof, pursuant to the accompanying Notice of Annual Meeting of Stockholders. The purposes of the Annual Meeting and the matters to be acted upon are set forth in the accompanying Notice of Annual Meeting of Stockholders. The Board of Directors is not currently aware of any other matters that will come before the Annual Meeting.

The mailing address of our principal executive offices is Synageva BioPharma Corp., 33 Hayden Avenue, Lexington, MA 02421. We will make arrangements with brokerage houses and other custodians, nominees and fiduciaries to send proxies and proxy materials to the beneficial owners of shares and will reimburse them for their expenses in so doing. Proxies may be solicited, without extra compensation, by officers, agents and employees of Synageva who may communicate with stockholders, banks, brokerage houses and others by telephone, facsimile, email or in person to request that proxies be furnished. All expenses incurred in connection with this solicitation will be borne by us. We have no present plans to hire special employees or paid solicitors to assist in obtaining proxies, but reserve the option of doing so. If any special employees or solicitors are retained, we will bear the expense of such retention.

All references in this Proxy Statement to “Synageva,” the “Company,” “we,” “us” and “our” refer to Synageva BioPharma Corp. (formerly known as Trimeris, Inc.) and its consolidated subsidiaries for periods after the closing of the reverse merger with Trimeris, Inc. (“Trimeris”) and Synageva BioPharma, Inc. (“Private Synageva”), a privately-held Delaware corporation (the “Merger”), on November 2, 2011, and to Private Synageva and its consolidated subsidiaries for periods prior to the closing of the Merger, unless the context requires otherwise.

Revocability and Voting of Proxy

A form of proxy for use at the Annual Meeting and a return envelope for the proxy are enclosed. Stockholders may revoke the authority granted by their execution of proxies at any time before such proxies are voted at the Annual Meeting by filing a written notice of revocation with the Secretary of Synageva, by mailing a duly executed proxy bearing a later date, by voting by phone (1-800-690-6903) or the internet (www.proxyvote.com) prior to the cut-off date described on the enclosed proxy, or by voting in person at the Annual Meeting. Shares of our common stock represented by executed and unrevoked proxies will be voted in accordance with the choice or instructions specified thereon. If a proxy card is signed and returned without any specifications, your shares will be voted in the manner recommended by our Board of Directors.

Record Date

The record date for voting is April 11, 2014. Only stockholders of record at the close of business on April 11, 2014 are entitled to notice of, and to vote at, the Annual Meeting and any adjournment of the Annual Meeting. On April 11, 2014, there were 33,005,251 shares of our common stock outstanding. Each share is entitled to one vote on each of the matters to be presented at the Annual Meeting. This Proxy Statement was mailed to stockholders of record on approximately April 23, 2014.

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Quorum and Required Vote

The holders of a majority of the outstanding shares of common stock entitled to vote, present in person or represented by proxy, will constitute a quorum at the Annual Meeting. Abstentions and broker non-votes will be counted for purposes of determining the presence or absence of a quorum. “Broker non-votes” are shares held by brokers or nominees that are present in person or represented by proxy, but not voted on a particular matter because (i) instructions have not been received from the beneficial owner and (ii) the brokers do not have discretionary voting authority to vote on such matter. A broker may not vote on “non-routine” matters without receiving specific voting instructions from the beneficial owner.

Broker discretionary voting. If shares are held by a broker, the broker will ask the beneficial owner for instructions to vote the shares. If instructions are provided, the broker must vote the shares as directed. If instructions are not provided, the broker’s ability to vote the shares depends on the proposal. At the Annual Meeting and any and all adjournments thereof, brokers may submit a vote on the ratification of the appointment of the independent registered accounting firm even if it does not receive instructions from the beneficial owner. For all other proposals, the broker may not vote unless the broker receives specific instructions from the beneficial owner. We urge each stockholder to provide instructions to its broker so that its votes may be counted on these important matters.

Proposal No. 1: Election of Directors. For the election of directors, you may either vote “for” a director or “withhold” your vote for such director. The affirmative vote of a majority of the shares of common stock present or represented and entitled to vote at the Annual Meeting, in person or by proxy is required for the election of each of the nominees. Broker non-votes will have no effect on the voting outcome with respect to the election of directors.

Proposal No. 2: Advisory Vote on the Compensation of Synageva’s Named Executive Officers. For the advisory vote to approve named executive officer compensation, you may either vote “for,” “against” or “abstain.” Because this proposal asks for a non-binding, advisory vote, there is no “required vote” that would constitute approval. We value the opinions expressed by our stockholders in this advisory vote, and our Compensation Committee, which is responsible for overseeing and administering our executive compensation programs, will consider the outcome of the vote when designing our executive compensation programs and making future compensation decisions for our named executive officers. Abstentions and broker non-votes, if any, will not have any effect on the results of those deliberations.

Proposal No. 3: Approval of the Company’s 2014 Equity Incentive Plan. For the proposal to approve the Company’s 2014 Equity Incentive Plan, you may either vote “for,” “against” or “abstain.” The affirmative vote of a majority of the shares of common stock present or represented and entitled to vote at the Annual Meeting, in person or by proxy, is required to approve Proposal No. 3. Abstentions will be treated as a vote “against” the proposed plan. Broker non-votes will not affect the voting outcome with respect to the proposed plan.

Proposal No. 4: Ratification of Synageva’s Independent Registered Public Accounting Firm. For the proposal to ratify the appointment of PricewaterhouseCoopers LLP as Synageva’s independent registered public accounting firm, you may either vote “for,” “against” or “abstain.” The affirmative vote of a majority of the shares of our common stock present or represented and entitled to vote at the Annual Meeting, in person or by proxy, is required to approve Proposal No. 4. Abstentions will be treated as a vote “against” Proposal No. 4. We do not expect there will be any broker non-votes on this matter as the approval of Proposal No. 4 is considered to be routine and a broker or other nominee is generally empowered to vote on such routine proposals. Consequently, it is unlikely that any broker non-votes will result.

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BENEFICIAL OWNERSHIP OF COMMON STOCK

The following table sets forth certain information as of April 11, 2014 (except as otherwise noted) regarding the beneficial ownership (as defined by the Securities and Exchange Commission, or SEC) of our common stock of: (i) each person known by us to own beneficially more than 5% of our outstanding common stock; (ii) each named executive officer listed in the Summary Compensation Table below; (iii) each director; and (iv) all directors, and executive officers of Synageva as a group.

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PROPOSAL NO. 1—ELECTION OF DIRECTORS

Eight directors have been nominated for election at the Annual Meeting to serve until the next annual meeting of stockholders and until their successors shall have been duly elected and qualified or until their earlier resignation or removal. In the event any of the nominees shall be unable to serve as a director, the shares represented by the proxy will be voted for such other candidate, if any, who is nominated by the Board of Directors to replace the nominee. All nominees have consented to be named in the Proxy Statement and have indicated their intent to serve if elected. The Board of Directors has no reason to believe that any of the nominees will be unable to serve.

Directors will be elected by a majority of the votes cast by the stockholders entitled to vote on the election of directors at the Annual Meeting.

THE BOARD OF DIRECTORS DEEMS PROPOSAL NO. 1 TO BE IN THE BEST INTERESTS OF SYNAGEVA AND ITS STOCKHOLDERS AND RECOMMENDS A VOTE “FOR” EACH NOMINEE.

GENERAL INFORMATION ABOUT THE BOARD OF DIRECTORS

Below please find information about the nominees for directors. In addition to the information presented below regarding each nominee’s specific experience, qualifications, attributes and skills that lead the Board of Directors to the conclusion that he should serve as a director, Synageva also believes that all of its director nominees have a reputation for integrity, honesty and adherence to high ethical standards. They have each demonstrated business acumen and an ability to exercise sound judgment. Finally, Synageva values their significant experience on other boards of directors.

Nominees

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Each director nominee, if elected, will hold office until the next annual meeting of stockholders and until his or her successor is elected and qualified or until his or her earlier resignation or removal. Mr. Patel is a party to an employment agreement with us. For the purposes of these biographies, the “Company” means the Company together with Trimeris.

Sanj K. Patel has served as President, Chief Executive Officer and a director of the Company since the Merger, and prior to that time served as the President and Chief Executive Officer and a director of Private Synageva since June 2008. He created the vision and strategy for the Company, launched its focus on rare diseases, and designed and initiated its lead program for LAL Deficiency in July 2008. He took the company public on the NASDAQ Global Market in November 2011 and since 2009, has raised over $800 million in capital. Mr. Patel has more than 20 years of experience in the pharmaceutical and biotech industries and has a combination of scientific, clinical and commercial skills. He joined the Company from Genzyme Corporation (1999-2008) where most recently he was the head of U.S. Sales, Marketing and Commercial Operations for Genzyme Therapeutics’ Lysosomal Storage Disorder franchise and led the U.S. launch of Myozyme^® in addition to sales and marketing responsibility for Cerezyme^®, Fabrazyme^® and Aldurazyme^®. Previously, Mr. Patel held several cross-functional senior leadership roles at Genzyme, including Vice President, Clinical Research and Head of the Global Clinical Research Operations Council. He was responsible for clinical operations and development for all cross-business Genzyme products and was instrumental in the path to commercialization for several treatments. Notably, Mr. Patel led the Fabrazyme clinical operations team and development program to FDA approval in April 2003. Prior to Genzyme, Mr. Patel held roles in clinical research and commercial development with increasing levels of responsibility at Burroughs Wellcome, Hoechst Marrion Roussel and Fujisawa Pharmaceuticals. Mr. Patel obtained his B.Sc. with Honors in Pure and Applied Biology (Biotechnology) from the University of the South Bank, London. He completed his post-graduate management and business degree, and doctorate level research program at Ealing College, London, and the Wellcome Foundation, respectively. Mr. Patel is a member of the Board of Directors for the Sarcoma Foundation of America, a non-profit organization, and Intercept Pharmaceuticals, Inc., a publicly traded biotechnology company. Mr. Patel’s extensive healthcare industry leadership experience combined with his specific expertise in the development and commercialization of rare disease treatments benefit the Board of Directors.

Felix J. Baker, Ph.D. has served as a director of the Company since April 2004 and currently serves as Chairman of the Board of Directors. Previously, Dr. Baker was also a director of Private Synageva from October 2000 until the Merger and Chairman of the Board of Directors of Private Synageva from 2003 until the Merger. Dr. Baker is Co-Managing Member of Baker Bros. Advisors, LP. Dr. Baker and his brother, Julian Baker, started their fund management careers in 1994 when they co-founded a biotechnology investing partnership with the Tisch Family. In 2000, they founded Baker Bros. Advisors LP. Dr. Baker holds a B.S. and a Ph.D. in Immunology from Stanford University, where he also completed two years of medical school. In addition to the Company, Dr. Baker is a director of Genomic Health and Seattle Genetics, Inc., both of which are publicly traded biotechnology companies. Dr. Baker was previously a director of AnorMED Inc., Ardea Bioscience, Inc., Conjuchem Inc. and Neurogen Corporation, which were publicly traded companies during Dr. Baker’s service. Dr. Baker is a highly experienced director who has served on the board of directors of several public and private biopharmaceutical corporations, which contributes to the knowledge base and oversight of the Board of Directors.

Stephen R. Biggar, M.D., Ph.D. has served as a director of the Company since the Merger, and prior to that time served as a director of Private Synageva since May 2004. Since October 2006, Dr. Biggar has served as a Partner at Baker Bros. Advisors LP, a registered investment adviser focused on long-term investments in life sciences companies. Dr. Biggar joined Baker Bros. Advisors LP in 2000. Prior to joining Baker Bros., Dr. Biggar received an M.D. and a Ph.D. in Immunology from Stanford University and received a B.S. in Genetics from the University of Rochester. Dr. Biggar also serves as a director for ACADIA Pharmaceuticals, a publicly traded biotechnology company. Dr. Biggar’s experience with life science investments and his medical and scientific training enhances the composition of the Board of Directors.

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Stephen R. Davis has served as a director of the Company since June 2007. In May 2013, Mr. Davis joined Heron Therapeutics, Inc. (formerly known as A.P. Pharma), a publicly traded company, as Executive Vice President and Chief Operating Officer and has served as a member of Heron Therapeutics’ board of directors since June 2012. Previously, Mr. Davis was Executive Vice President and Chief Operating Officer at Ardea Biosciences, Inc. He has completed numerous strategic transactions between biotechnology and pharmaceutical companies, including the recent $1.26 billion acquisition of Ardea by AstraZeneca PLC. Prior to Ardea, Mr. Davis served as President and Chief Executive Officer of Neurogen Corporation, a biopharmaceutical company acquired by Ligand Pharmaceuticals. Before becoming Neurogen’s Chief Executive Officer, Mr. Davis served in numerous executive roles at Neurogen completing multiple collaboration and asset acquisition and sale transactions with global pharmaceutical companies. Mr. Davis is also a director of Furiex Pharmaceuticals Inc., a publicly traded biotechnology company. Previously, Mr. Davis practiced as a corporate and securities attorney with a Wall Street law firm and as a Certified Public Accountant with a major accounting firm. Mr. Davis received his Bachelor of Science degree in Accounting from Southern Nazarene University and a J.D. from Vanderbilt University. Mr. Davis has extensive knowledge of the Company’s industry, as evidenced by his professional background. The Board of Directors benefits from Mr. Davis’ experience in several senior positions at biopharmaceutical corporations and particular expertise in corporate finance.

Thomas R. Malley has served as a director of the Company since the Merger, and prior to that time served as a director of Private Synageva since October 2006. Since May 2007, Mr. Malley has served as President of Mossrock Capital, LLC, a private investment firm. From December 1998 to May 2007, Mr. Malley served with Janus Mutual Funds, including as Vice President and Portfolio Manager for the Janus Global Life Sciences Fund. From April 1991 to December 1998, Mr. Malley served as an equity analyst for Janus Mutual Funds. Mr. Malley previously served as a director of Cougar Biotechnology, Inc. from 2007 to 2009, which was a publicly traded company until Johnson & Johnson acquired the company in 2009. Mr. Malley also previously served as a director of Craig Hospital, a non-profit hospital, from 2007 to 2013 and St. Anthony Hospital, a non-profit hospital, from 2004-2009. Mr. Malley is also a director of Puma Biotechnology, Inc. and OvaScience, Inc. two publicly traded biotechnology companies, and is also a director of Project Cure, a non-profit organization. Mr. Malley holds a B.S. in Biology from Stanford University. Mr. Malley’s industry and investment experience benefits the Board of Directors.

Barry Quart, Pharm.D. has served as a director of the Company since June 2007. In May 2013, Dr. Quart joined Heron Therapeutics, Inc. (formerly known as A.P. Pharma) as Chief Executive Officer, and has served as a member of the board of directors at Heron Therapeutics, Inc. since June 2012. Prior to Heron Therapeutics, Inc., Dr. Quart was President and Chief Executive Officer, and Director of Ardea Biosciences, Inc., a publicly traded biopharmaceutical company, since co-founding the company in December 2006. Ardea was acquired by AstraZeneca PLC for $1.26 billion in June 2012. Previously, he was with Pfizer as Senior Vice President, Pfizer Global Research and Development and the director of Pfizer’s La Jolla Laboratories, where he was responsible for approximately 1,000 employees and an annual budget of almost $300 million. Prior to Pfizer’s acquisition of the Warner-Lambert Company, Dr. Quart was President of Research and Development at Agouron Pharmaceuticals, Inc., a division of the Warner-Lambert Company. Agouron was acquired by Warner-Lambert for $2.1 billion in 1999. Dr. Quart joined Agouron in 1993 and was instrumental in the development and registration of Viracept, which went from the laboratory bench to new drug application approval in 38 months. Dr. Quart received his Pharm.D. degree from the University of California, San Francisco. Dr. Quart has extensive knowledge of the Company’s industry, as evidenced by his experience in the biotechnology and pharmaceuticals industries. The Board of Directors benefits from Dr. Quart’s broad experience in senior management roles, as well as his experience as a director of several biopharmaceutical corporations.

Thomas J. Tisch has served as a director of the Company since June 2012. Mr. Tisch has served as the Managing Partner of Four Partners, a private investment firm, since 1992. He has served as the Chancellor of Brown University since July 2007, and he is also a trustee of New York University Medical Center and a director of Sears Holding Corporation, a publicly traded company. Mr. Tisch brings financial and general business expertise to the Board of Directors from his position at a private investment firm.

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Peter Wirth has served as a director of the Company since June 2012. Mr. Wirth is Chairman of FORMA Therapeutics Holdings, LLC, a cancer drug discovery company. Mr. Wirth has served as a Director of Lysosomal Therapeutics, Inc., a private neurodegeneration company, since January 2012, and as a Director of Aura Biosciences, Inc., a private cancer drug discovery company, since December 2013. During 2012, Mr. Wirth was an Advanced Leadership Fellow at Harvard University. From January 1996 through May 2011, Mr. Wirth was a senior executive at Genzyme Corporation, most recently Executive Vice President, Legal and Corporate Development, Chief Risk Officer and Corporate Secretary. His responsibilities included oversight of the corporate development and legal departments, and management of the company’s enterprise risk management activities. Prior to joining Genzyme, Mr. Wirth was a partner at Palmer & Dodge, a Boston law firm, where he was head of the firm’s biotechnology practice group and served as Genzyme’s outside general counsel since 1982. Mr. Wirth received his B.A. from the University of Wisconsin-Madison in 1972 and his J.D. from Harvard Law School in 1975. Mr. Wirth brings financial, legal and extensive knowledge of the company’s industry which will benefit the Board of Directors.

Executive Officers

The following is certain biographical information for the executive officers currently employed by the Company who are not discussed above:

Carsten Boess has served the Company as Senior Vice President and Chief Financial Officer since the Merger and prior to that time served Private Synageva in such capacity since May 2011. He is responsible for leading the Company’s financial and strategic operations. Mr. Boess has more than 20 years of financial operations and management experience in the life sciences industry with diversified experience across a broad field of areas both in the U.S. and internationally. Prior to joining the Company, Mr. Boess served in the roles of Chief Financial Officer and Vice President, International of Insulet Corporation, respectively (June 2006-2011) and has also served in the following capacities: Chief Financial Officer of Alexion Pharmaceuticals, Inc., Executive Vice President of Finance for Serono, Inc. and Vice President Finance, International Operations for Novo Nordisk. Mr. Boess has significant international experience having served as head of finance of companies in the U.S., Denmark, China, Switzerland, and France. He also headed the expansion of Insulet’s business internationally in the role of Vice President, International. Mr. Boess earned a Bachelor’s and Master’s degree in economics and finance from the University of Odense, Denmark.

Anthony G. Quinn, MBChB (M.D.), Ph.D., FRCP serves as the Company’s Executive Vice President and Chief Medical Officer and is also Head of Research and Development. Dr. Quinn has served as an executive officer of the Company since the Merger and prior to that time served Private Synageva in such capacity since August 2009. Prior to joining the Company, he was Vice President and Global Head of Clinical Research & Exploratory Development for Inflammation at Roche. While at Roche, Dr. Quinn managed programs in rheumatology and respiratory indications in exploratory development, and biomarker and translational medicine activities in the late clinical and registration phase for MabThera™/Rituxan™, Actemra™ and Ocrelizumab. Dr. Quinn joined Roche in 2005 to build the translational medicine and exploratory development capabilities at the site across a broad range of therapeutic areas including CNS, virology and inflammation. Prior to joining Roche, he was Director of Experimental Medicine at AstraZeneca, Charnwood in the UK, and before that he was

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Professor of Dermatology at Barts & The London School of Medicine, London, England. He has authored or co-authored more than 50 peer-reviewed journal articles, book chapters, reviews and editorials, predominantly on Hedgehog signaling and the molecular biology of non-melanoma skin cancer. He received his Bachelor of Medical Science with First Class Honours and his M.B.Ch.B. (M.D.) with commendation from the University of Dundee, UK. Dr. Quinn trained in internal medicine, dermatology and molecular biology at the University of Newcastle upon Tyne and was also awarded his Ph.D. there. He completed a postdoctoral fellowship at University of California, San Francisco, and is a fellow of the Royal College of Physicians London.

Mark Goldberg, M.D. serves as Executive Vice President, Medical and Regulatory Strategy of the Company. Dr. Goldberg has served as an executive officer of the Company since the Merger and prior to that time served Private Synageva in such capacity since September 2011 and served as a director of Private Synageva from October 2008 until December 2011. Dr. Goldberg joined the Company from Genzyme Corporation, where he most recently served as Senior Vice President, Clinical Development and Global Therapeutic Group Head, Oncology and Personalized Genetic Health. While at Genzyme, he played a central role in the development and approval of some of the benchmark therapies for rare diseases, including Fabrazyme^®, Aldurazyme^®, Myozyme^® and Lumizyme^®. Prior to working at Genzyme, he was a full time staff physician at Brigham and Women’s Hospital and Dana Farber Cancer Institute, where he still holds appointments. He is also a Clinical Associate Professor of Medicine at Harvard Medical School. Dr. Goldberg is a board-certified medical oncologist and hematologist and has more than 50 published papers. Reporting directly to Mr. Patel and working very closely with Dr. Quinn, the Company’s Chief Medical Officer, Dr. Goldberg plays a central role in developing medical and regulatory strategy and ensuring the successful progress and advancement of pipeline programs. Dr. Goldberg received his A.B. (magna cum laude) from Harvard College and his M.D. (cum laude) from Harvard Medical School.

Glen Williams has served as Senior Vice President of Global Technical Operations with responsibility for our global supply chain, including oversight of the Manufacturing and Quality organizations since September 2012. He brings over 25 years of industry experience, most recently as Chief Operating Officer for Caliber Biotherapeutics. Mr. Williams was previously Senior Vice President of Technical Operations for Biolex Therapeutics focusing on the development of human therapeutic proteins through the use of a high level plant system for therapeutic protein production. Prior to joining Biolex, Mr. Williams was the Vice President of Manufacturing and General Manager for Biogen Idec’s Research Triangle Park facilities where he was responsible for site-wide manufacturing operations for new and marketed recombinant therapeutic proteins. In his ten years with Biogen Idec, Mr. Williams built and successfully licensed two biopharmaceutical production facilities with multiple regulatory authority approvals in addition to launching three commercial biopharmaceutical products, two of which exceeded one billion dollars in annual revenues. In addition to managing major GMP biomanufacturing and supply chain operations, he has an extensive background in the design, construction, startup and licensing of new biopharmaceutical production facilities. Mr. Williams received his M.B.A. from Central Michigan University and his B.S. in Mechanical Engineering from The Ohio State University.

MEETINGS AND COMMITTEES OF THE BOARD OF DIRECTORS

The Board of Directors conducts its business through meetings of the full Board of Directors and through committees, consisting of standing audit, compensation and nomination and governance committees. In addition to the standing committees, the Board of Directors from time to time establishes special purpose committees.

During the fiscal year ended December 31, 2013, Synageva’s Board of Directors held five meetings, the Audit Committee held four meetings, the Compensation Committee held four meetings, and the Nomination and Governance Committee did not hold any meetings. No director attended less than 75% of the aggregate of the total number board meetings held during such director’s term or the total number of meetings of the committees on which such director served during such director’s term. Although the Board of Directors has no formal policy

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regarding the attendance of its members at the Annual Meeting, it has been the practice of the Board of Directors to hold a meeting on the same date as our annual meetings of stockholders to encourage all directors to attend the annual meeting. Mr. Patel, Dr. Baker and Mr. Wirth attended the 2013 annual meeting.

The Board of Directors has determined that seven of its eight current members (Drs. Baker, Biggar, and Quart and Messrs. Davis, Malley, Tisch and Wirth) are “independent directors” as that term is defined under the NASDAQ Stock Market Listing Standards and the SEC rules and regulations. During all of the regularly scheduled meetings, the Board of Directors met in executive session where only the independent directors were present without any members of Synageva’s management. Neither we nor any of our subsidiaries are party to any material proceedings to which any of our directors, officers, affiliates, 5% or more stockholders, or any of their respective associates are a party. We do not believe that any of our directors, officers, affiliates, 5% or more stockholders, or any of their respective associates are adverse to us or any of our subsidiaries or have a material interest that is adverse to us or any of our subsidiaries.

Audit Committee

In August 2005, the Board of Directors established a separately designated standing Audit Committee to review the internal accounting procedures of Synageva, consult with our independent registered public accounting firm and review the services provided by the independent registered public accounting firm. The Audit Committee operates pursuant to a charter, which has been approved and adopted by the Board of Directors and is reviewed and reassessed annually by the Audit Committee. A copy of the Audit Committee charter is available on our website at: www.synageva.com. Messrs. Davis, Malley and Wirth are the current members of the Audit Committee. Mr. Malley serves as chairman. The Board of Directors has determined that each member of the Audit Committee is an “independent director” as that term is defined under the NASDAQ Stock Market Listing Standards and the SEC rules and regulations. Our Board of Directors has also determined that Mr. Malley and Mr. Davis are “audit committee financial experts” as that term is defined under the NASDAQ Stock Market Listing Standards and the SEC rules and regulations.

Compensation Committee

In June 2004, the Board of Directors established a Compensation Committee. The Compensation Committee reviews compensation practices, determines and approves compensation of the Chief Executive Officer and all other executive officers, and administers our equity compensation and incentive plans. Mr. Patel provides recommendations for salary changes, individual components of annual incentive cash bonus awards and equity awards for each of our executive officers other than himself. These recommendations are presented to, reviewed by, modified or accepted by, our Compensation Committee and recommended for full Board approval. The Compensation Committee operates pursuant to a charter which has been approved and adopted by the Board of Directors and is reviewed and reassessed annually by the Compensation Committee. A copy of the Compensation Committee charter is available on our website at: www.synageva.com. Dr. Baker, Mr. Davis and Mr. Wirth are the current members of the Compensation Committee. Dr. Baker serves as chairman. The Board of Directors has determined that each member of the Compensation Committee is an “independent director” as that term is defined under the NASDAQ Stock Market Listing Standards and the SEC rules and regulations.

Nomination and Governance Committee

The Board of Directors established the Nomination and Governance Committee to provide leadership and guidance to Synageva, review and recommend new directors to the Board of Directors, establish the necessary committees of the Board of Directors to provide oversight to Synageva and make recommendations regarding committee membership. The Nomination and Governance Committee adopted a charter in 2012, which is available on our website at: www.synageva.com. Dr. Baker, Dr. Biggar and Mr. Malley are the current members of the Nomination and Governance Committee. Dr. Baker serves as chairman. The Board of Directors has determined that each member is an “independent director” as that term is defined under the NASDAQ Stock Market Listing Standards.

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CORPORATE GOVERNANCE

Process for Selecting Nominees and Stockholder Nominations

It is the policy of the Nomination and Governance Committee to consider candidates for the Board of Directors recommended by Nomination and Governance Committee members and other members of the Board of Directors, management, our stockholders, third-party search firms and any other appropriate sources. As a stockholder, you may recommend a person for consideration as a nominee for director by writing to the Nomination and Governance Committee of the Board of Directors, c/o Synageva BioPharma Corp., 33 Hayden Avenue, Lexington, MA 02421, Attention: Secretary. Recommendations must be received by December 24, 2014 to be considered for the 2015 Annual Meeting of Stockholders. Recommendations must include the name and address of the stockholder making the recommendation, a representation setting forth the number of shares of our common stock beneficially owned by the recommending stockholder, a statement from the recommended nominee that expresses his or her intent to serve on the Board of Directors if elected, biographical information about the recommended nominee, any other information the stockholder believes would be helpful to the Nomination and Governance Committee in evaluating the recommended nominee and a description of all arrangements or understandings between the recommending stockholder and each nominee and any other person concerning the nomination. The evaluation process for nominees recommended by stockholders is the same as for candidates recommended by any other source.

Board of Directors Diversity

We recognize that diversity enhances the overall effectiveness of the Board of Directors by ensuring that different perspectives, skills and experiences are presented to directors and to management. The Nomination and Governance Committee considers diversity, including gender, ethnic background, country of citizenship and professional experience, and recommending, as necessary, measures that contribute to a Board of Directors that, as a whole, reflects a range of viewpoints, backgrounds, skills, experience and expertise. The Nomination and Governance Committee reviews Board of Directors composition on an annual basis to ensure that the Board of Directors reflects the knowledge, experience, skills, expertise and diversity required for the Board of Directors to fulfill its duties.

Director Qualifications

The Board of Directors seeks independent directors who represent a range of viewpoints, backgrounds, skills, experience and expertise. Members of the Board of Directors should possess the attributes necessary to be an effective director, including the following: personal and professional integrity, high ethical values, sound business judgment, demonstrated exceptional business and professional skills and experience, teamwork and a commitment to the long-term interests of Synageva and its stockholders. In evaluating candidates, the Nomination and Governance Committee also considers potential conflicts of interest, diversity, the requirement to maintain a Board of Directors that is composed of a majority of independent directors, and the extent to which a candidate would fill a present or anticipated need. In any particular situation, the Nomination and Governance Committee may focus on individuals possessing a particular background, experience or qualifications that the committee believes would be important to enhance the effectiveness of the Board of Directors.

Board Leadership Structure

The Board of Directors does not have a fixed policy regarding the separation of the positions of Chairman and Chief Executive Officer and believes that it should maintain the flexibility to select the Chairman and its Board leadership structure, from time to time, based on the criteria that it deems to be in the best interests of the Company and its stockholders. Currently, Synageva separates the positions of Chairman, which is held by Dr. Baker, and the Chief Executive Officer, which is held by Mr. Patel. The Board of Directors believes by separating positions at this time, Mr. Patel may devote his attention to Synageva’s day-to-day operations and strategy while Dr. Baker can take responsibility for leading the Board of Directors.

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Board of Directors’ Role in Risk Oversight

The Board of Directors is responsible for overseeing Synageva’s risk management processes. The full Board of Directors performs a periodic risk assessment with management to review the primary risks facing Synageva and to manage the activities of Synageva in identifying and mitigating such risks. Management identifies risks in multiple areas, including compliance, financial, strategic, political and operational risks, and on a regular basis the Board of Directors reviews together with management. The Board of Directors recognizes that Synageva is subject to both internal and external risks, within and outside its control, and that management and the Board of Directors should regularly seek to identify those risks and mitigate to the extent possible. As part of the risk management process and consistent with its standing oversight role, each committee of the Board of Directors considers the risks within its areas of responsibility and assists the full Board of Directors in its oversight of the risk management process. In reviewing Synageva’s compensation programs, Synageva reviews whether compensation policies and practices create risks that are reasonably likely to have a material adverse effect on Synageva.

Stockholder Communications with the Board of Directors

Our Board of Directors has provided a process for stockholders to send it communications. Stockholders who wish to send communications to the Board of Directors, or any particular director, should address such communications to the Board of Directors, c/o Synageva BioPharma Corp., 33 Hayden Avenue, Lexington, MA 02421, Attention: Secretary. All such communications should include a representation from the submitting stockholder setting forth the stockholder’s address and the number of shares of Synageva common stock beneficially owned by the stockholder.

The Secretary will (i) monitor communications from stockholders and (ii) provide copies or summaries of such communications to the Board of Directors, or the director to whom such communication is addressed, as the Secretary considers appropriate. Each stockholder communication will be forwarded if it relates to a substantive matter and includes suggestions or comments that the Secretary considers to be important for the directors, or director, to know. In general, stockholder communications relating to corporate governance and long-term corporate strategy are more likely to be forwarded than stockholder communications relating to personal grievances and matters as to which we tend to receive repetitive or duplicative communications. The Board of Directors will give appropriate attention to written communications on such issues and will respond as appropriate.

Code of Ethics

We adopted the Synageva BioPharma Corp. Code of Business Conduct and Ethics that applies to directors, officers and employees of Synageva and its subsidiaries and complies with the applicable SEC rules and regulations and the NASDAQ Stock Market Listing Standards. Our code of ethics is located on our website at: www.synageva.com. Amendments or waivers to our code of ethics will be promptly disclosed on our website and as required by applicable laws, rules and regulations of the SEC and NASDAQ.

Corporate Governance Guidelines

The Board of Directors believes that sound governance practices and policies provide an important framework to assist it in fulfilling its duty to stockholders. The Nomination and Governance Committee has adopted Corporate Governance Guidelines and relies on the guidelines to provide that framework. The guidelines are not absolute rules, and can be modified to reflect changes in Synageva’s organization or business environment. The Nomination and Governance Committee periodically review the guidelines and if necessary, modifies the guidelines to reflect current good governance practices and policies. Synageva’s Corporate Governance Guidelines are located on our website at: www.synageva.com.

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Section 16(a) Beneficial Ownership Reporting Compliance

Section 16(a) of the Exchange Act requires our directors, executive officers and persons who beneficially own more than 10% of our common stock, to file initial reports of beneficial ownership of our stock and reports of changes in beneficial ownership of our stock with the SEC. Executive officers, directors and greater than 10% beneficial owners are required by the SEC to furnish us with copies of all Section 16(a) forms they file.

Based solely upon a review of the copies of such forms furnished to us and written representations from our executive officers and directors, we believe that during the year ended December 31, 2013, all Section 16(a) filing requirements applicable to our executive officers, directors and greater than 10% beneficial owners were complied with on a timely basis, except that there was an inadvertent failure to timely report an indirect purchase of shares through trusts by Mr. Tisch on January 9, 2013 and a same-day stock option exercise for the purchase and sale of shares by Dr. Goldberg on March 1, 2013.

EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

Introduction

This Compensation Discussion and Analysis section discusses our executive officer compensation program and the decisions made with respect to 2013 compensation for our executive officers identified in the Summary Compensation Table (referred to as our named executive officers). Our named executive officers for 2013 were:

The material elements of 2013 compensation paid to our named executive officers includes:

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Relationship Between 2013 Company Performance and Compensation Decisions

The compensation of our executive officers for 2013 is based on the performance of the Company and our individual executives during the year. It is also consistent with our compensation objectives — to focus our officers on the achievement of key business objectives and to align their interests with those of our stockholders. The key corporate objectives applicable to our executive officers for 2013 and the key corporate accomplishments considered in the determination of executive compensation by the Compensation Committee for each objective were as follows:

Advancement of Synageva’s Lead Program, Sebelipase Alfa

In 2013, we successfully achieved multiple important corporate and product development milestones. Success in achieving these milestones enabled us to continue to develop our lead program, sebelipase alfa, and our pipeline programs, moving the company closer toward becoming a fully integrated, global organization focused on the development, manufacturing and commercialization of therapies for patients suffering from rare and devastating diseases.

Pipeline Development

In 2013, we advanced our next program, SBC-103, an enzyme replacement therapy for mucopolysaccharidosis type IIIB (MPS IIIB), or Sanfilippo B. Specifically, we produced preclinical data demonstrating that dosing with SBC-103 reduces the accumulation of substrate in the brain of a Sanfilippo MPS IIIB animal model with various dosing approaches. These data were presented at the 9th Annual LDN WORLD Symposium in February 2013. We also advanced our preclinical pipeline programs closer toward IND-enabling studies.

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In addition, we further strengthened our balance sheet through underwritten public offerings in 2013 yielding net proceeds of $281 million.

2013 Compensation Highlights and Key Decisions

Our compensation philosophy is to align each executive’s compensation with our short-term and long-term performance and to provide the compensation and incentives needed to attract, motivate and retain key executives who are crucial to our long-term success. Consistent with this philosophy, a significant portion of the total compensation opportunity for each of our executives is directly related to performance factors that measure our progress against our key corporate objectives, as well as the level of achievement of individual goals developed by the Compensation Committee and approved by the Board of Directors at the beginning of the year in support of such objectives.

Base salaries should be paid in the range of the market median. In 2013, the base salaries for our named executive officers, other than Mr. Williams, and Mr. Glynn were considered to be in the range of the market median and were increased between 3% and 4% for merit in alignment with the average increase for other employees of the Company and in line with industry trends. Mr. Williams’ salary was increased 14% to bring him closer to the market median of our peer group, which is identified and discussed below. Mr. Glynn’s increase was limited to 1% because he joined the Company in September 2012.

Annual cash incentive awards reflected 2013 company and individual performance. We seek to tie a substantial portion of an executive’s overall compensation to our performance. In 2013, as described above, we executed on our strategic plan and produced strong results and significant value creation for our stockholders, and achieved multiple strategic, operational and product objectives. The Compensation Committee determined that cash incentive awards above the target amounts described below were warranted and consistent with our philosophy of paying cash incentive bonuses based on performance.

Long-term incentive awards, particularly stock options, are an important element of compensation and value creation. We believe that equity compensation should be targeted in the range of the 75^th percentile of our market peers. The Compensation Committee believes that a practice of awarding LTIs to Synageva executives will contribute to long-term successful company performance. In particular, the use of stock options aligns the interests of our executives with our stockholders because our executives will only realize a return on an option if Synageva’s stock price increases. Stock options do not guarantee value to the executive. We continued our practice commenced in 2012 to grant long-term equity incentive awards at or around our annual meeting, which is typically mid-year, in order to align the timing of these grants with the equity awards made to our non-employee members of the Board of Directors as well as allow a mid-year review of Company results prior to the issuance of these awards.

Summary of Compensation Analysis

Each year, the Compensation Committee reviews and establishes Synageva’s overall executive compensation strategy. The Compensation Committee evaluates Synageva’s existing compensation program and considers whether changes are necessary or advisable due to changed conditions, company performance, best practices or otherwise. As part of the evaluation, the Compensation Committee considers whether new programs or strategies should be introduced.

Based on its assessment, and in consideration of many of the factors described throughout this discussion, the Compensation Committee believes that the executive compensation program substantially achieved its objectives for 2013 and is well aligned with the compensation philosophies described below. The Compensation Committee did not recommend any changes to its executive compensation program for 2013.

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Key decisions regarding Synageva’s 2013 executive officer compensation were made in December 2012, June 2013 and December 2013.

Executive Compensation Philosophy

The primary objective of our executive compensation policy is to attract, retain and motivate the key executives necessary for our short- and long-term success. We seek to tie short- and long-term cash and equity incentives to employee performance, including the achievement of measurable corporate and individual objectives, and to align executives’ incentives with stockholder value. The Compensation Committee seeks to implement its compensation programs in a way that ties a substantial portion of an executive’s overall compensation to Synageva’s performance and each element of an individual’s compensation is evaluated and determined in consideration of such person’s contribution and performance. With the exception of Mr. Patel, who is guaranteed a minimum annual cash incentive payment of 25% of his base salary, no executive is guaranteed a cash or equity incentive award and such incentives are determined at levels that the Compensation Committee believes drives performance.

The Compensation Committee approves compensation programs based on certain compensation philosophies, including the following:

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Role of the Compensation Committee

Our executive compensation policy is set by the Compensation Committee, and the Compensation Committee is also responsible for approving the compensation of our named executive officers for recommendation to the full Board of Directors. The Compensation Committee regularly reassesses and reviews our compensation policy and programs.

Compensation determinations are not based on a rigid mathematical formula but rather multiple factors. The Compensation Committee undertakes an annual benchmarking exercise to compare each executive’s proposed compensation to that of individuals in similar positions at a peer group of companies. Generally, the Compensation Committee seeks to target base salary and target annual cash incentives for each executive in the range of the median of the peer group and LTIs in the range of the 75^th percentile.

The Compensation Committee also evaluates, at the end of the year, the annual performance of Synageva and the Chief Executive Officer (CEO) by assessing the achievement of Synageva’s objectives, which are approved at the beginning of each year, and determining the level of achievement which is calculated as a percentage of the objective. The Compensation Committee reviews and approves the CEO’s evaluation of individual performance of Synageva’s other executive officers, including an assessment of achievement of individual objectives, which are also approved at the beginning of each year. Finally, the Compensation Committee takes into account each individual’s contributions in resolving unanticipated matters, general economic conditions, and any other factors the Compensation Committee deems relevant. Per its charter, the Compensation Committee may form subcommittees and delegate authority to any subcommittee or other administrator, as appropriate.

Role of Executives in 2013 Compensation Decisions

It is Synageva’s policy that no executive officer participates or makes recommendations regarding his or her own compensation.

A small number of executives generally attend Compensation Committee meetings, including the Company’s CEO and the Senior Vice President, Human Resources. Executive sessions of the Compensation Committee are conducted without any Synageva executives.

The CEO, with limited staff and management support, works with the Compensation Committee and our compensation consultant to determine compensation recommendations and achievement of individual performance goals for our executive officers other than himself. His recommendations are submitted to the Compensation Committee for review, discussion, modification and recommendation to the full Board of Directors.

The Compensation Committee is responsible for evaluating and determining CEO compensation for recommendation to the full Board of Directors and works directly with the compensation consultant, with limited support from Synageva staff and without input from the CEO.

Role of the Compensation Consultant

In 2013, after evaluating the performance of its compensation consultant, Compensia, Inc. (Compensia), the Compensation Committee again retained Compensia as an external, independent executive compensation consultant. The Compensation Committee uses the analysis prepared by the consultant as part of its periodic

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review of Synageva’s executive and director compensation practices. The consultant reports directly to the Compensation Committee, and the Compensation Committee has the final authority to hire and terminate the consultant. The Compensation Committee evaluates the consultant annually.

Our consultant attends certain meetings of the Compensation Committee, as requested, and may communicate with the Compensation Committee chairman between meetings; however, the Compensation Committee makes all decisions regarding the compensation of our executive officers.

Compensia provided advice, information and recommendations directly to, and at the request of, the Compensation Committee, and the Compensation Committee’s decisions regarding the components and amounts of executive and director compensation were informed by the analysis and input of Compensia. The Compensation Committee assessed Compensia’s independence in 2013. The Compensation Committee determined that Compensia was independent and there were no conflicts of interest that would impact the advice to the Compensation Committee from Compensia and the representative of Compensia who advises the committee on executive compensation matters.

Components of Compensation—General

The components of our executive compensation program include the following:

The Compensation Committee believes that each component of compensation should be used in a manner that drives certain conduct. The Compensation Committee believes that base salary should provide a secure, fixed amount of compensation to attract and retain highly talented individuals, while the second element of cash compensation, annual cash incentives, should be used as a tool to motivate executives to achieve short-term, annual goals. Meanwhile, LTIs more closely align the interests of our executives with those of our stockholders.

When establishing annual incentive compensation opportunities, the Compensation Committee evaluates the 50^th and 75^th percentiles of the peer group for similar positions to understand where these opportunities fall relative to the competitive market. In making compensation determinations, the Compensation Committee considers each component of compensation in relation to the total amount of compensation paid and whether the compensation package as a whole adequately compensates each executive for Synageva’s performance during the past year and each executive’s contribution to such performance.

In consideration of Synageva’s 2012 performance, the Compensation Committee sought to achieve 2013 total compensation between the 50^th and 75^th percentiles of the market peers, even if certain components were below or above such level. Generally, 2013 base salary and target annual cash incentives for each named executive were in the range of the median for our peer group at the time such compensation was determined, while LTIs were above the market median and in the range of the 75^th percentile.

We discuss each component of our compensation program in more detail below, including the rationale for 2013 compensation decisions.

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Peer Group Analysis

The Compensation Committee believes that executive compensation should be considered in comparison with compensation paid by market peers to ensure that Synageva is competitive with other companies who compete with us for talent. The Compensation Committee, together with its compensation consultant, reviews the peer group on a regular basis and approves the peer group annually. The Compensation Committee believes that the factors listed below are the most important to consider for its determination of the Synageva peer group:

The Compensation Committee endeavors to select peer companies that exhibit all of the factors set forth above but recognizes that it cannot develop a peer group in which all companies exhibit all factors. All of Synageva’s peer companies are in the same industry and have the same or similar Standard Industrial Classification (SIC) Code. However, the similarities between Synageva and a particular peer company with respect to any of the other factors listed above, such as commercial capabilities, will vary. Further, with respect to a particular factor, such as orphan disease focus, there may be no similarity. The Compensation Committee believes that in some cases the peer group should be designed to purposefully include companies that are not identical to Synageva. For example, the Compensation Committee believes that the peer group should include companies with both higher as well as lower market capitalization than Synageva to fairly represent the median compensation paid to executives at such companies as a group. However, in some cases, the lack of similarity is not by design of the peer group, but rather because there are not a sufficient number of companies that are similar to Synageva with respect to such factor. For example, not all companies in Synageva’s peer group are in the same stage of clinical development. The Compensation Committee believes that it is not possible to eliminate such differences entirely and recognizes the possibility that shifts in its peer group selection could influence executive compensation decisions. The Compensation Committee seeks to mitigate such risk by not relying entirely on any one or two factors, but to include companies that represent as many of the factors listed above as possible. The Compensation Committee also seeks to avoid reliance on one or two factors alone, such as commercial capabilities and market capitalization, because doing so would likely alter, possibly significantly, the results of the benchmarking exercise and the Compensation Committee’s determinations. The Compensation Committee believes that the mix of factors listed above results in a balanced and representative peer group, taking into

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consideration Synageva’s operations and needs, and the Compensation Committee expects that use of such peer group will result in compensation decisions that support the Company’s compensation philosophy and objectives.

The Compensation Committee generally compares the compensation of each named executive officer in relation to both the median and the 75th percentile of the peer group for similar positions at the peer group. The Compensation Committee also takes into account various factors such as the unique characteristics of the individual’s position, and any succession and retention considerations.

Over the course of 2013, the Compensation Committee, together with Compensia, reviewed a peer group that had been selected in 2012 based on its evaluation of several factors, including the factors described above under Peer Group Analysis. No changes were made to the peer group for 2013.

The peer group used by the Compensation Committee to assist in the determination of 2013 annual incentive bonuses, 2013 long-term incentive awards, and 2014 base salary compensation is comprised of the following companies:

Compensia collected its data from peer group proxy statements and from the 2012 Radford Global Life Sciences Survey.

The Compensation Committee places significant emphasis on the use of comparative market data. The Compensation Committee uses the market information to ensure that compensation for executives is at least competitive with the peer group. The information also provides a framework for the Compensation Committee in evaluating and awarding compensation in circumstances of superior performance. Compensia provides peer group data for each Synageva executive by matching the Synageva executive with executives in the peer group with similar titles and similar job responsibilities. The Compensation Committee also recognizes that differences exist between the duties of Synageva’s executives and those matched at the peer group of companies. The Compensation Committee considers such differences when evaluating compensation and performance.

2013 Compensation Components

As a baseline for awarding compensation and prior to making annual executive compensation decisions, the Compensation Committee evaluates Synageva’s performance for the prior year by assessing if, and the extent to which, Synageva achieved or failed to achieve the corporate goals approved by the Compensation Committee and the Board of Directors. To assist in the determination of 2014 base salaries and achievement of targets for annual incentive awards, the Compensation Committee evaluated Synageva’s performance in December 2013 and determined that Synageva achieved 130% of its approved corporate goals for 2013. Specifically, Synageva:

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In June 2013, the Compensation Committee recommended for the approval by the Board of Directors the granting of stock options for all then serving executive officers. In December 2013, the Compensation Committee reviewed the 2013 corporate goals and the goals of the individual then-serving named executive officers, other than Mr. Patel, in order to determine the payment of 2013 annual cash incentive awards and also approved 2014 base salaries and 2014 annual cash incentive targets, subject to the approval of the Board of Directors. In approving and awarding these components of compensation, the Compensation Committee determined that Synageva exceeded its 2013 corporate goals, had a strong performance in 2013, and that the Compensation Committee should seek to achieve total compensation for each executive commensurate with those accomplishments.

Base Salary

Base salary represents a secure, fixed component of an executive’s compensation. Determinations of base salary levels for our executives are established based on the position, the scope of responsibilities, and the prior relevant background, training and experience of each individual. Base salaries take into account an annual review of marketplace competitiveness with the peer group. We believe that base salaries for our executives are competitive in the industry and that Synageva’s base salary levels have contributed to our ability to successfully attract and retain highly talented executives.

In determining 2013 and 2014 base salaries, the Compensation Committee relied on the market comparisons provided by its compensation consultant. As with each other component of compensation, an executive’s base salary is evaluated together with other components of the executive’s compensation in the aggregate to ensure that the executive’s total compensation is in line with our overall compensation philosophy.

On an individual basis, 2013 and 2014 annual increases in base salary reflect marketplace competitiveness levels, the industry’s annual competitive pay practices, an individual’s contributions to Synageva’s overall performance, and length of service. Utilizing the peer group data, 2013 and 2014 base salaries of all positions for which there was available and adequate data was evaluated and compared to Synageva’s base salaries during 2012 and 2013.

In 2013, the base salaries for our named executive officers, other than Mr. Williams and Mr. Glynn, were considered to be in the range of the market median and were increased between 3% and 4% for merit in alignment with the average increase for other employees of the Company and in line with industry trends. Mr. Williams’ salary was increased 14% to bring him closer to the market median of our peer group and Mr. Glynn’s increase was limited to 1% because he joined the Company in September 2012. In setting base salaries for 2014 and consistent with previous annual base salary evaluations, the Compensation Committee determined that base salaries for the named executive officers should be within the range of the market median. In December 2013, the Compensation Committee and the Board of Directors approved increases of 5% for Mr. Patel, and 4% each for Mr. Boess and Mr. Williams. Dr. Quinn and Dr. Goldberg were each promoted to the

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level of Executive Vice President and received increases of 7% and 3.5% respectively. Dr. Goldberg and the Company also agreed to a reduced time commitment for Dr. Goldberg of three days per week, effective January 1, 2014, and that Dr. Goldberg would therefore be paid 60% of his salary effective January 1, 2014.

Annual Incentives Bonuses

Synageva seeks to deliver target annual cash incentives in the range of the 50th percentile of the peer group. In 2013, and in consideration of Synageva’s strong performance, the amount of annual incentives actually paid to our named executive officers was at or above the market median of the peer companies.

Annual cash incentive bonuses are designed to reward annual achievements and to be commensurate with each executive officer’s scope of responsibilities, demonstrated leadership, management abilities and effectiveness in his role. Annual cash incentive bonuses are also intended to retain executives, to motivate executives to achieve short-term (annual) success, and to reward, in the short-term, significant contributions to the success of Synageva. While Synageva’s policy is to pay a significant portion of its senior executives’ cash compensation in the form of annual incentive bonuses, no senior executive of Synageva, with the exception of Mr. Patel, our CEO, who is guaranteed a minimum bonus payout of 25% of his salary, is guaranteed an annual incentive bonus.

As noted above, the Compensation Committee first approves each executive’s target (a percentage of base salary) at the beginning of each calendar year and establishes annual corporate performance goals as well as individual goals for the executive officers, other than Mr. Patel. Corporate and individual goals are proposed by management, reviewed and approved by the Compensation Committee and also approved by the Board of Directors. The Compensation Committee considers and assigns a relative weight to each corporate goal to appropriately focus efforts on corporate goals that are intended to enhance stockholder value and an overall weight of 10% for individual goals, except for Mr. Patel who is only evaluated on achievement of the corporate goals. In December 2013, prior to approving 2013 annual incentive bonuses, the Compensation Committee evaluated Synageva’s 2013 performance by assessing if, and the extent to which, Synageva achieved or failed to achieve the corporate goals approved by the Compensation Committee and the Board of Directors for 2013. In assessing the performance of management against pre-determined goals, the Compensation Committee and the Board of Directors may consider circumstances such as the over-achievement of goals and management’s ability to capitalize on newly identified opportunities or manage through obstacles not foreseen at the time the goals were established. The Compensation Committee determined that Synageva’s 2013 performance, in total, exceeded the approved corporate goals.

In December 2012, the Compensation Committee and the Board of Directors approved the following annual cash incentive bonus targets as a percentage of base salary for 2013: 60% for Mr. Patel, 40% for each of Dr. Quinn and Dr. Goldberg, and 35% for each of Mr. Boess, Mr. Williams and Mr. Glynn. Ms. Secor’s bonus target was negotiated at the time of hire and was set at 40% under her employment agreement. Ms. Secor did not receive a performance bonus in 2013 as she was not employed through the end of the year. The Compensation Committee believed that targets should be set in a manner consistent with Synageva’s compensation philosophy of paying for performance, and maintaining competitive compensation arrangements in order to retain and motivate our executives. The Compensation Committee set targets in the range of the median of the peer group. Actual annual cash incentive bonuses for 2013 were approved and paid in December 2013 based on the achievement of the corporate and individual goals.

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Set forth below are the 2013 corporate goals, the weight assigned and Synageva’s achievement:

To optimize achievement of corporate goals, individual goals are set in support of annual corporate goals for all executives other than our CEO, Mr. Patel, and represent 10% of each named executive officer’s annual incentive bonus payment. The annual corporate goals represent the other 90% of each named executive officer’s goals. Individual goals for 2013 overlapped with our corporate goals for 2013 and consisted of sub-goals designed to achieve our corporate goals.

Prior to the December 2013 Compensation Committee meeting, Mr. Patel reviewed in detail the performance of each named executive officer, excluding himself, and considered such individual’s contributions to Synageva’s success in 2013 and recommended the compensation to be paid to each individual based on the achievement of the individual goals set forth above. In making his recommendations, Mr. Patel worked closely with the Compensation Committee, relied on data provided by the compensation consultant, and received limited support from staff and other members of management.

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The Compensation Committee considered 2013 to be a strong year for Synageva. In 2013, the Company attained key strategic milestones that the Compensation Committee expects to provide long-term value to Synageva’s business, to patients and to stockholders. In particular, Synageva:

Mr. Patel recommended annual cash incentives based on strong individual and corporate performance in 2013. Synageva exceeded 2013 objectives and each executive made important contributions to Synageva’s 2013 achievements. The Compensation Committee discussed Mr. Patel’s recommendations for the named executive officers and determined that annual cash incentive decisions for the named executive officers, including Mr. Patel, should reflect Synageva’s strong performance in 2013 and recognition of significant achievements.

In December 2013, Mr. Patel, Dr. Quinn, Dr. Goldberg, Mr. Boess and Mr. Williams received annual incentive bonuses with respect to 2013 performance of $468,874, $193,073, $191,318, $159,611, and $141,120, respectively, representing 130%, 127%, 126%, 127% and 126% of the target annual incentive bonus amounts, respectively. In December 2013, Mr. Glynn was still employed by Synageva, but was no longer serving as an executive officer. He received an annual incentive bonus with respect to 2013 performance of $119,306 representing 90% of his target annual incentive bonus.

2013 Long-Term Incentive Awards

Synageva uses stock options as its long-term incentives (LTIs). The Compensation Committee reviews and approves LTI grant guidelines for all positions and levels throughout the global organization other than executives (senior vice presidents and above). The LTI grant guidelines are established to ensure that Synageva’s grant practices are competitive in each jurisdiction where our employees are located. We review market data by position, level and geographical region and establish guidelines and award values that we believe enable us to attract, retain and motivate a talented, values driven workforce.

An eligible employee will receive an annual award after the employee’s performance is evaluated and the actual LTI value delivered for each individual recipient is based on the LTI guidelines and an assessment of an individual’s performance.

The Compensation Committee has not established LTI grant guidelines for its executives, including the named executive officers. Together with the compensation consultant, the Compensation Committee conducts a detailed benchmarking exercise to evaluate each executive’s award levels compared to market peers. In determining LTI awards for executives, the Compensation Committee considers:

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As is the case when the amount of base salary and annual cash incentive opportunity is determined, when determining LTI values, a review of all of the executive’s compensation is conducted to ensure that an executive’s total compensation conforms to our overall philosophy and objectives.

Options are granted with an exercise price equal to the fair market value of Synageva’s common stock on the date of grant and, accordingly, will only have value if Synageva’s stock price increases. Generally, LTI awards vest over four years and the individual must be employed by Synageva as an employee, director or consultant for such awards to vest. The Compensation Committee believes that conditioning these awards on employment also serves as a valuable retention tool.

The Compensation Committee believes that long-term equity-based incentive awards are a critical element of compensation. However, like a short-term cash incentive award (or cash bonus), a long-term equity incentive award is a variable component of each employee’s compensation and no individual, including any executive, is guaranteed to receive an award or a certain value. In determining 2013 grant levels, which were evaluated in May 2013, the Compensation Committee recognized the importance of maintaining this alignment and considered Synageva’s strong 2012 and to date 2013 performance. The Compensation Committee believed that it was appropriate to set 2013 grant levels in the range of the 75^th percentile of the peer group.

The Compensation Committee believes that its practice of awarding LTIs to Synageva executives has contributed to long-term successful performance, which has been demonstrated through substantial value creation for Synageva’s stockholders. Starting in 2012, LTI awards are granted at or around our annual meeting which is typically mid-year. The timing of these awards align the timing of management and board LTI awards as well as allow a mid-year review of company results prior to the awards.

LTIs were granted to executives (and other employees and the board of directors) in June 2013. The Compensation Committee approved LTIs to Mr. Patel, Mr. Boess, Dr. Quinn, Dr. Goldberg, Mr. Williams and Mr. Glynn in the amounts set forth in the table under the heading “Grants of Plan-Based Awards.” Ms. Secor received a new hire stock option grant that was negotiated at the time of her hire in the amount set forth in the table under the heading “Grants of Plan-Based Awards.” Her grant did not vest as of her departure date and expired unexercised.

Termination Based Compensation

We provide severance payments and other benefits to our executives under written employment agreements if they are terminated without cause or in certain other instances, including in connection with a change of control. We believe that executives, particularly a company’s most senior executives, often face challenges securing new employment following termination and that non-financial severance terms identify important continuing obligations of both Synageva and our executive officers, such as protection against competition and solicitation. In addition, severance provisions related to a change of control also assist in retaining high quality executives and keeping them focused on their responsibilities during any period in which a change of control may be contemplated or pending, and in providing the executives a sense of security and trust that they will be treated fairly during such transactions. For details on the severance payments our executives are entitled to, please refer to the section entitled “Potential Payments Upon Termination or Change of Control” in this proxy statement.

Personal Benefits

Our executives are eligible for the benefit programs provided to all employees, such as medical, dental, vision, life and disability insurance benefits. We do not provide, and executives are not entitled to, perquisites such as permanent lodging, cars or defraying the cost of personal entertainment or family travel, other than in 2012 for Mr. Williams. Mr. Williams received certain benefits in connection with his relocation to Lexington, MA upon his hire in 2012. The amounts paid to Mr. Williams in 2012 for such benefits are reflected in the Summary Compensation Table.

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Assessment of Risk

The Compensation Committee monitors the risks associated with our executive compensation programs and individual compensation decisions. The Compensation Committee has concluded that risks associated with our compensation policies and practices are within our ability to effectively monitor and manage and that the risks are not reasonably likely to have a material adverse effect on Synageva.

Other Compensation Matters

The Compensation Committee regularly reviews, assesses and discusses Synageva’s compensation programs to determine whether its practices and policies achieve Synageva’s compensation objectives and are consistent with the Company’s compensation philosophies. The Compensation Committee believes that compensation programs should be adjusted and should evolve over time due to many considerations and factors, including Synageva’s performance, Synageva’s growth, stockholder sentiment and feedback, compensation and corporate governance best practices, risk mitigation strategies, and regulatory developments. The Compensation Committee believes that Synageva’s current compensation practices have contributed to Synageva’s strong short- and long-term performance, including Synageva’s exceptional performance in 2013, and have facilitated significant stockholder value creation.

COMPENSATION COMMITTEE REPORT

The Compensation Committee of the Board of Directors reviewed and discussed the Compensation Discussion and Analysis required by Item 402(b) of Regulation S-K with management and, based on such review and discussions, the Compensation Committee recommended to the Board of Directors that the Compensation Discussion and Analysis be included in this Proxy Statement.

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SUMMARY COMPENSATION TABLE

The following table shows the compensation paid to the Company’s Principal Executive Officer, Principal Financial Officer and its three highest compensated executive officers other than the Principal Executive Officer and Principal Financial Officer for services rendered in 2013, 2012 and 2011, as applicable. The table also includes two additional individuals who would have been among the three most highly compensated executive officers except for the fact that they were not serving as executive officers of the Company as of December 31, 2013.

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Chief Executive Officer’s Employment Agreement

Following the Merger, the Board of Directors approved the terms of a new employment agreement with Sanj K. Patel, the Company’s President and Chief Executive Officer, effective as of November 2, 2011 (the “Patel Agreement”).

Under the terms of the Patel Agreement, Mr. Patel in entitled to a base salary, which was set at $601,120 per year for 2013, an annual cash bonus with a target level of 60%, and a minimum payout level of 25%, of his annual base salary. Synageva may also grant Mr. Patel equity awards each year. The performance targets related to Mr. Patel’s annual cash bonus and the terms and conditions of his equity awards are to be determined by the Compensation Committee and approved by the Board, and the actual amount of Mr. Patel’s annual cash bonus shall be determined in good faith by the Compensation Committee based on actual corporate and individual performance. Under the Patel Agreement, if Synageva terminates Mr. Patel’s employment without cause (as defined below) or Mr. Patel terminates his employment for good reason (as defined below), Mr. Patel will be entitled to the following severance:

If Synageva terminates Mr. Patel’s employment without cause or he resigns for good reason during the 12 months following a change of control, as defined in the agreement, Mr. Patel will be entitled to the following severance:

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Under the Patel Agreement, “cause” means: (i) gross negligence or willful misconduct in performance of the executive’s duties to the Company, where such gross negligence or willful misconduct has resulted in material damage to the Company or any of its affiliates or successors; (ii) commission of any act of fraud, embezzlement or professional dishonesty with respect to the Company or any of its affiliates; (iii) commission of a felony or crime involving moral turpitude; (iv) material breach of any provision of this Agreement or any other written agreement between the executive and the Company; or (v) failure to comply with lawful directives of the Board of Directors, which has caused damage to the Company or any of its affiliates or successors.

Mr. Patel would be entitled to terminate his employment for “good reason” under the Patel Agreement if any of the following events occur without Mr. Patel’s written consent: (i) the assignment to Mr. Patel of duties materially inconsistent with his title, position, status, reporting relationships, authority, duties or responsibilities; (ii) any action by the Company which results in a diminution in Mr. Patel’s title, position, status, reporting relationships, authority, duties or responsibilities, other than insubstantial or inadvertent actions not taken in bad faith which are remedied by the Company promptly after receipt of notice thereof given by Mr. Patel; (iii) a requirement that Mr. Patel relocate his primary reporting location to a location more than 50 miles from the location of the Company’s offices in Lexington, Massachusetts; (iv) any failure by the Company to comply with certain provisions of the Patel Agreement, other than insubstantial or inadvertent failures not in bad faith which are remedied by the Company promptly after receipt of notice thereof given by Mr. Patel; (v) a material diminution in the budget over which Mr. Patel has responsibility; or (vi) a breach by the Company of any written agreement between the Company and Mr. Patel.

Executive Employment Agreements with Carsten Boess, Anthony G. Quinn, Mark Goldberg, Glen Williams and Michael Glynn

Following the Merger, the Board of Directors approved the terms of new employment agreements for all Senior Vice Presidents of the Company (the “Executive Employment Agreements”). Mr. Boess, Dr. Quinn and Dr. Goldberg entered into employment agreements, effective November 2, 2011. Mr. Williams and Mr. Glynn each entered into an employment agreement effective upon his hire on September 24, 2012, and September 3, 2012, respectively.

Pursuant to the Executive Employment Agreements, the Company will pay Mr. Boess, Dr. Quinn, Dr. Goldberg, Mr. Williams and Mr. Glynn’s annual base salaries in amounts determined by the Compensation Committee, and each executive shall be eligible to receive an annual cash bonus of up to 35%, 40%, 40%, 35% and 35% of their annual base salaries, respectively. If Synageva terminates the employment of Mr. Boess, Dr. Quinn, Dr. Goldberg, Mr. Williams or Mr. Glynn without cause, as defined below, Synageva will accelerate the vesting of all of the executive’s unvested equity awards by 12 months and the executive will receive (i) cash severance payable in a lump sum equal to 9 months of his base salary for Mr. Boess, Mr. Williams and Mr. Glynn or 12 months of his base salary for Dr. Quinn and Dr. Goldberg; and (ii) a pro-rata share of his target annual cash bonus for the year in which the termination occurs. If Synageva terminates the executive without cause during the 12 months following a change of control, as defined in the agreement, the executive will receive (i) cash severance payable in a lump sum equal to 12 months of his base salary; (ii) a lump sum payment equal to the target annual cash bonus for the year in which the termination occurs; (iii) a one-time bonus of $16,500; and (iv) acceleration of all unvested equity then held by the executive by 12 months and full vesting of all awards that were assumed or substituted in the change of control.

Under the Executive Employment Agreements, “cause” means: (i) gross negligence or willful misconduct in performance of the executive’s duties to the Company, where such gross negligence or willful misconduct has resulted in material damage to the Company or any of its affiliates or successors; (ii) commission of any act of

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fraud, embezzlement or professional dishonesty with respect to the Company or any of its affiliates; (iii) commission of a felony or crime involving moral turpitude; (iv) material breach of any provision of the Executive Employment Agreement or any other written agreement between the executive and the Company; or (v) failure to comply with lawful directives of the CEO, which has caused damage to the Company or any of its affiliates or successors.

Annual Cash Bonus Plan

The Company has established an Annual Cash Bonus Plan that is administered by the Compensation Committee. Executive officers and other employees of the Company and its affiliates are eligible to participate. The Compensation Committee selects who may receive bonus awards, the criteria used to determine whether the recipient is entitled to the award, the amount payable, the relative performance period to which the award relates and other terms and conditions as the Compensation Committee deems appropriate with respect to the award.

2013 GRANTS OF PLAN-BASED AWARDS

The following table sets forth information regarding awards made to our named executive officers during the year ended December 31, 2013:

SO = Stock Option

CBP = Cash Bonus Plan

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OUTSTANDING EQUITY AWARDS AT 2013 FISCAL YEAR-END

The following table shows grants of stock options and grants of unvested stock awards outstanding on December 31, 2013, the last day of our fiscal year, to each named executive officer.

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OPTION EXERCISES AND STOCK VESTED FOR FISCAL 2013

The following table shows exercises of stock options and restricted stock vesting for the year ended December 31, 2013, for each of the named executive officers.

Retirement Benefits

We do not have any pension or qualified or non-qualified defined benefit plans that apply to our named executive officers. We offer a tax-qualified retirement plan (the “401(k) Plan”) to eligible employees. The 401(k) Plan permits eligible employees to defer up to 90% of their annual eligible compensation, subject to certain limitations imposed by the Internal Revenue Code of 1986, as amended. Following a 6-month waiting period for eligibility, the employees’ elective deferrals are immediately vested and non-forfeitable in the 401(k) Plan. In any plan year, we will contribute to each participant a matching contribution equal to 100% of the first 3% of the participant’s compensation that he or she has contributed to the plan and 50% of the next 2% of the participant’s compensation that he or she has contributed to the plan.

Other Elements of Compensation and Perquisites

In order to attract, retain and pay market levels of compensation, we provide our executive officers and other employees the following benefits and perquisites:

Life and Disability Insurance

We provide each named executive officer disability and/or life insurance that we may from time to time make available to other executive employees of the same level of employment.

Other

We make available certain other perquisites or fringe benefits to all eligible employees, including our named executive officers, such as professional society dues, cell phones and food and recreational fees incidental to official company functions, including board meetings.

Potential Payments Upon Termination or Change of Control

We have entered into certain agreements and maintain certain plans that may require us to make certain payments and/or provide certain benefits to our named executive officers in the event of a termination of employment or a change of control. See “Potential Payments Upon Termination or Change of Control” below for a description of the severance and change in control arrangements for Mr. Patel, Mr. Boess, Dr. Quinn,

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Dr. Goldberg, Mr. Williams and Mr. Glynn. Each named executive officer would only be eligible to receive severance payments if such officer signed a general release of claims. The following tables summarize the potential payments to each named executive officer assuming that one of the events described in the table occurred. The tables assume that the relevant event occurred on December 31, 2013 and, in calculating the amounts due to the executive in connection with such event, use the closing price of a share of our common stock, $64.72, on such date, and that all outstanding equity awards were assumed, substituted, or cashed out in the change of control. However, the executive’s employment was not terminated on December 31, 2013 under such agreement and a change in control did not occur on that date. There can be no assurance that a termination of employment, a change in control or both would produce the same or similar results as those set forth below if either or both of them occur on any other date or at any other price, or if any other assumption used in calculating the benefits set forth below is not correct in fact.