ACHN 2018 Proxy Supplement

SUPPLEMENT TO PROXY STATEMENT FOR THE 2018 ANNUAL MEETING OF STOCKHOLDERS TO BE HELD ON MAY 31, 2018 The following information relates to the proxy statement (the “Proxy Statement”) of Achillion Pharmaceuticals, Inc., a Delaware corporation (“we,” “Achillion,” “us,” or the “Company”), as filed by the Company with the Securities and Exchange Commission (the “SEC”) and furnished to stockholders of the Company in connection with the solicitation of proxies by the Company’s board of directors (the “Board of Directors”) for the Company’s 2018 Annual Meeting of Stockholders (the “Annual Meeting”). All capitalized terms used in this supplement to the Proxy Statement (this “Supplement”) and not otherwise defined herein have the respective meanings ascribed to such terms in the Proxy Statement. This Supplement, which amends the Proxy Statement, is being filed with the SEC and being made available to stockholders of the Company on May 3, 2018. The Company will hold the Annual Meeting as originally scheduled on May 31, 2018. The Proxy Statement provides information about the matters you will be asked to consider and vote on at the Annual Meeting, except that information with respect to Proposal 5 is set forth in this Supplement. Only stockholders of record as of the close of business on April 16, 2018 are entitled to receive notice of and to vote at the Annual Meeting. The Proxy Statement contains important additional information, and this Supplement should be read in conjunction with the Proxy Statement. Appointment of Joseph Truitt as Chief Executive Officer; Director Nominee On May 1, 2018, Milind S. Deshpande ceased to serve as the Company’s Chief Executive Officer and he resigned as a director, effective immediately. The Board of Directors appointed Joseph Truitt, the Company’s President and Chief Operating Officer, as Chief Executive Officer, effective May 1, 2018. The Board of Directors also elected Mr. Truitt as a Class III director to fill the vacancy created by Dr. Deshpande’s resignation as a director. Mr. Truitt was elected to serve on the Board of Directors until the Annual Meeting and until his successor is duly elected and qualified. Dr. Desphande had been nominated by the Board of Directors for re-election as a Class III director at the Annual Meeting. However, as a result of his resignation as a director, Dr. Deshpande’s name has been withdrawn from nomination for re-election as a Class III director at the Annual Meeting and no vote with respect to the election of him as a director will occur at the Annual Meeting. Our Board of Directors has nominated Mr. Truitt for election at the Annual Meeting as a Class III director. Because this change adds Mr. Truitt to the slate of directors proposed to be elected at the Annual Meeting, we are providing you with additional information in this Supplement and an amended proxy card to allow stockholders to vote on the election of Mr. Truitt as a Class III director. For technical reasons related to the tallying of votes, the election of Mr. Truitt as a director is being considered as a separate proposal (Proposal 5). Jason S. Fisherman, who had also been nominated by our Board of Directors for re-election as a Class III director, will continue to stand for re-election as a Class III director at the Annual Meeting under Proposal 1. PROPOSAL 5—ELECTION OF CLASS III DIRECTOR The Proxy Statement is hereby amended to provide, as a new Proposal 5 to be voted on by stockholders, for the election of Joseph Truitt as a Class III director. If elected, Mr. Truitt will hold office until our annual meeting of stockholders in 2021 and until his successor is duly elected and qualified. Mr. Truitt has indicated his willingness to serve, if elected; however, if he should be unable to serve, the shares of common stock represented by proxies may be voted for a substitute nominee designated by the Board of Director. Below is biographical and certain other information with respect to Mr. Truitt, including his principal occupation and business experience for the past five years. The information presented below for Mr. Truitt regarding his specific experience, qualifications, attributes and skills led our Nominating and Corporate Governance Committee and our Board of Directors to conclude that he should serve as a director. In addition, we believe that Mr. Truitt possesses the attributes or characteristics described under the “Director Nomination Process” in the Proxy Statement that the Nominating and Corporate Governance Committee expects of each director, including the candidate’s integrity, business acumen, knowledge of our business and industry, experience, diligence, age, lack of conflicts of interest, the ability to act in the interests of all stockholders and whether the candidate enhances the diversity of our Board of Directors. Joseph Truitt, age 53 . Mr. Truitt has served as our President and Chief Operating Officer from February 2018 until his appointment as our Chief Executive Officer and as a member of the Board of Directors on May 1, 2018. In September 2017, Mr. Truitt was promoted to Chief Operating Officer and in February 2018 he was promoted to President and Chief Operating Officer. Prior to his promotion to Chief Operating Officer in September 2017, Mr. Truitt had served as our Chief Commercial