UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 14A INFORMATION

(Rule 14a-101)

PROXY STATEMENT PURSUANT TO SECTION 14(a) OF

THE SECURITIES EXCHANGE ACT OF 1934

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¨ Preliminary Proxy Statement

¨ Definitive Proxy Statement

ý Definitive Additional Materials

¨ Soliciting Material under 240.14a-12

¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))

LIGAND PHARMACEUTICALS INCORPORATED

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www.envisionreports.com/LGND Step 1: Go to www.envisionreports.com/LGND to view the materials. Step 2: Click on Cast Your Vote or Request Materials. Step 3: Follow the instructions on the screen to log in. Vote by Internet • Go to www.envisionreports.com/LGND • Or scan the QR code with your smartphone • Follow the steps outlined on the secure website Stockholder Meeting Notice 02BFFB + + Important Notice Regarding the Availability of Proxy Materials for the Ligand Pharmaceuticals Incorporated Stockholder Meeting to be Held on Monday, May 23, 2016 Under Securities and Exchange Commission rules, you are receiving this notice that the proxy materials for the annual stockholders’ meeting are available on the Internet. Follow the instructions below to view the materials and vote online or request a copy. The items to be voted on and location of the annual meeting are on the reverse side. Your vote is important! This communication presents only an overview of the more complete proxy materials that are available to you on the Internet. We encourage you to access and review all of the important information contained in the proxy materials before voting. The proxy statement and annual report to stockholders are available at: : Easy Online Access — A Convenient Way to View Proxy Materials and Vote When you go online to view materials, you can also vote your shares. Step 4: Make your selection as instructed on each screen to select delivery preferences and vote. When you go online, you can also help the environment by consenting to receive electronic delivery of future materials. Obtaining a Copy of the Proxy Materials – If you want to receive a copy of these documents, you must request one. There is no charge to you for requesting a copy. Please make your request for a copy as instructed on the reverse side on or before May 9, 2016 to facilitate timely delivery. . LIGAND PHARMACEUTICALS INCORPORATED IMPORTANT ANNUAL MEETING INFORMATION 1234 5678 9012 345 NNNNNNNNNNNN NN NN NN NN N NNNNNN C 1234567890 C O Y 000004 MR A SAMPLE DESIGNATION (IF ANY) ADD 1 ADD 2 ADD 3 ADD 4 ADD 5 ADD 6 ENDORSEMENT_LINE______________ SACKPACK_____________

Here’s how to order a copy of the proxy materials and select a future delivery preference: Paper copies: Current and future paper delivery requests can be submitted via the telephone, Internet or email options below. Email copies: Current and future email delivery requests must be submitted via the Internet following the instructions below. If you request an email copy of current materials you will receive an email with a link to the materials. PLEASE NOTE: You must use the number in the shaded bar on the reverse side when requesting a set of proxy materials. g Internet – Go to www.envisionreports.com/LGND. Click Cast Your Vote or Request Materials. Follow the instructions to log in and order a copy of the current meeting materials and submit your preference for email or paper delivery of future meeting materials. g Telephone – Call us free of charge at 1-866-641-4276 and follow the instructions to log in and order a paper copy of the materials by mail for the current meeting. You can also submit a preference to receive a paper copy for future meetings. g Email – Send email to investorvote@computershare.com with “Proxy Materials Ligand Pharmaceuticals Incorporated” in the subject line. Include in the message your full name and address, plus the number located in the shaded bar on the reverse, and state in the email that you want a paper copy of current meeting materials. You can also state your preference to receive a paper copy for future meetings. To facilitate timely delivery, all requests for a paper copy of the proxy materials must be received by May 9, 2016. . Stockholder Meeting Notice Ligand Pharmaceuticals Incorporated Annual Meeting of Stockholders will be held on Monday, May 23, 2016 at 11119 N. Torrey Pines Rd., Suite 200, La Jolla, CA 92037, at 8:30 a.m. Local Time. Proposals to be voted on at the meeting are listed below along with the Board of Directors’ recommendations. The Board of Directors recommends a vote “FOR ALL” Director nominees and “FOR” Proposals 2, 3 and 4: 1. Election of Directors Nominees: 01 Jason M. Aryeh 02 Todd C. Davis 03 John L. Higgins 04 John W. Kozarich 05 John L. LaMattina 06 Sunil Patel 07 Stephen L. Sabba 2. Ratification of Appointment of Independent Registered Accounting Firm. 3. Approval of the amendment and restatement of Ligand Pharmaceuticals Incorporated’s 2002 Stock Incentive Plan. 4. Approval, on a non-binding advisory basis, of the compensation of Ligand Pharmaceuticals Incorporated’s named executive officers. PLEASE NOTE – YOU CANNOT VOTE BY RETURNING THIS NOTICE. To vote your shares you must vote online or request a paper copy of the proxy materials to receive a proxy card. If you wish to attend and vote at the meeting, please bring this notice with you. 02BFFA

Using a black ink pen, mark your votes with an X as shown inthis example. Please do not write outside the designated areas. X LIGAND PHARMACEUTICALSINCORPORATED 02BFCE 1 U P X + Annual Meeting Proxy Card . +A Proposals — The Board of Directors recommends a vote “FOR ALL” Director nominees and “FOR” Proposals 2, 3 and 4. For Against Abstain2. Ratification of Appointment of Independent Registered Accounting Firm. For Against Abstain4. Approval, on a non-binding advisory basis, of thecompensation of Ligand PharmaceuticalsIncorporated’s named executive officers. 1. Election of Directors Mark here to WITHHOLDvote from all nomineesMark here to voteFOR all nominees For All EXCEPT - To withhold authority to vote for anynominee(s), write the name(s) of such nominee(s) below. _____________________________________________ 01 - Jason M. Aryeh 02 - Todd C. Davis 03 - John L. Higgins04 - John W. Kozarich 05 - John L. LaMattina 06 - Sunil Patel07 - Stephen L. Sabba Change of Address — Please print your new address below. Comments — Please print your comments below.B Non-Voting Items Meeting AttendanceMark the box to the rightif you plan to attend theAnnual Meeting.Authorized Signatures — This section must be completed for your vote to be counted. — Date and Sign BelowCNOTE: Please sign as name appears hereon. Joint owners should each sign. When signing as attorney, executor, administrator, trustee or guardian, please give full title as such.Signature 1 — Please keep signature within the box. Signature 2 — Please keep signature within the box.Date (mm/dd/yyyy) — Please print date below. IMPORTANT ANNUAL MEETING INFORMATION In their discretion, the named proxies are authorized to vote on any other business properly broughtbefore the meeting and at any adjournments or postponements thereof. Nominees: 3. Approval of the amendment and restatement of Ligand PharmaceuticalsIncorporated’s 2002 Stock Incentive Plan. 1234 5678 9012 345 MM MM MM MM M MMMMMMM MR A SAMPLE (THIS AREA IS SET UP TO ACCOMMODATE140 CHARACTERS) MR A SAMPLE AND MR A SAMPLE ANDMR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE ANDMR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE AND MMMMMMMMMMMM 000000000.000000 ext000000000.000000 ext000000000.000000 ext 000000000.000000 ext000000000.000000 ext000000000.000000 ext C123456789MMMMMMMMMMMMMMM C 1234567890 J N T2 7 6 2 9 0 1 000004 MR A SAMPLEDESIGNATION (IF ANY)ADD 1ADD 2ADD 3ADD 4ADD 5ADD 6 ENDORSEMENT_LINE______________ SACKPACK_____________ q IF YOU HAVE NOT VOTED VIA THE INTERNET OR TELEPHONE, FOLD ALONG THE PERFORATION, DETACH AND RETURN THE BOTTOM PORTION IN THE ENCLOSED ENVELOPE.q Electronic Voting InstructionsAvailable 24 hours a day, 7 days a week!Instead of mailing your proxy, you may choose one of the votingmethods outlined below to vote your proxy. VALIDATION DETAILS ARE LOCATED BELOW IN THE TITLE BAR.Proxies submitted by the Internet or telephone must be received by11:59 PM, Eastern Time, on May 22, 2016.Vote by Internet• Go to www.envisionreports.com/LGND• Or scan the QR code with your smartphone• Follow the steps outlined on the secure website Vote by telephone• Call toll free 1-800-652-VOTE (8683) within the USA, US territories &Canada on a touch tone telephone• Follow the instructions provided by the recorded message

. THIS PROXY IS SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS OFLIGAND PHARMACEUTICALS INCORPORATED The undersigned hereby appoints John L. Higgins and Charles S. Berkman, as proxies, jointly and severally, with full power of substitution to vote all sharesof stock which the undersigned is entitled to vote at the Annual Meeting of Stockholders of Ligand Pharmaceuticals Incorporated to be held at 8:30 a.m.local time at Ligand Pharmaceuticals Incorporated located at 11119 N. Torrey Pines Rd., Suite 200, La Jolla, CA 92037 on Monday, May 23, 2016, or at anypostponements or adjournments thereof, as specified on the reverse side, and to vote in their discretion on such other business as may properly come beforethe Meeting and any adjournments thereof. The Board of Directors recommends a vote FOR all the nominees listed and FOR Proposals 2, 3 and 4. (Continued and to be marked, dated and signed, on the other side) Proxy — LIGAND PHARMACEUTICALS INCORPORATED Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting:The Notice and Proxy Statement and Annual Report are available at http://www.envisionreports.com/LGND. q IF YOU HAVE NOT VOTED VIA THE INTERNET OR TELEPHONE, FOLD ALONG THE PERFORATION, DETACH AND RETURN THE BOTTOM PORTION IN THE ENCLOSED ENVELOPE.q