ACHN 2018 Proxy Supplement

ACHILLION PHARMACEUTICALS, INC. 300 George Street New Haven, Connecticut 06511 AMENDED NOTICE OF 2018 ANNUAL MEETING OF STOCKHOLDERS To Be Held on May 31, 2018 To our stockholders: We invite you to attend our 2018 annual meeting of stockholders, which will be held at our offices at 300 George Street, New Haven, Connecticut 06511 on Thursday, May 31, 2018 at 9:00 a.m., local time. At the meeting, stockholders will consider and act upon the following matters: 1. To elect Jason Fisherman, M.D. as a Class III Director for a term to expire at our 2021 annual meeting of stockholders or until his successor is duly elected and qualified; 2. To approve, on an advisory basis, our executive compensation; 3. To approve an amendment and restatement of our 2015 Stock Incentive Plan; 4. To ratify the selection of PricewaterhouseCoopers LLP as our independent registered public accounting firm for the current fiscal year; 5. To elect Joseph Truitt as a Class III Director for a term to expire at our 2021 annual meeting of stockholders or until his successor is duly elected and qualified; and 6. To transact such other business as may properly come before the meeting or any adjournment thereof. Stockholders of record at the close of business on April 16, 2018, the record date for the annual meeting, are entitled to notice of, and to vote at, the meeting. Your vote is important regardless of the number of shares you own. All stockholders are cordially invited to attend the meeting in person. Whether or not you expect to attend the meeting, we hope you will take the time to vote your shares. If you are a stockholder of record, you may vote over the Internet or by completing and mailing the enclosed amended proxy card in the envelope provided. If your shares are held in “street name,” that is, held for your account by a broker or other nominee, you will receive instructions from the holder of record that you must follow for your shares to be voted. You may revoke your proxy at any time prior to its exercise at the annual meeting. The proxy statement, which was first sent to stockholders on or about April 20, 2018, the attached supplement to proxy statement and our 2017 Annual Report on Form 10-K are also available to our stockholders electronically via the Internet at www.achillionproxymaterials.com. Each stockholder should take the time to review the attached supplement to proxy statement and the proxy statement and complete and return the enclosed amended proxy card. Our stock transfer books will remain open for the purchase and sale of our common stock. By Order of the Board of Directors, Martha E. Manning, Esq. Corporate Secretary New Haven, Connecticut May 3, 2018