Exhibit 10.1

WARNING: The following actions may trigger Austrian stamp duty:

“Substitute Document” means any signed document in writing by a party to this document (including further agreements, letters, faxes or email) referencing a Stamp Duty Sensitive Document (including other Substitute Documents) or the transactions documented in such Stamp Duty Sensitive Document.

Contact the legal department / legal advisors prior to making a reference to this Amendment or the transactions documented therein (including fax or email and even if the written reference is only for personal purposes and not directed to third parties) and obtain confirmation, that no stamp duty will be incurred by such action.

CONSENT AND FOURTH AMENDMENT TO CREDIT AGREEMENT

This CONSENT AND FOURTH AMENDMENT TO CREDIT AGREEMENT (this “Amendment”), is made and entered into as of June 22, 2026, by and among LIGAND PHARMACEUTICALS INCORPORATED, a Delaware corporation (the “Borrower”), the other Loan Parties party hereto, the Lenders party hereto (the “Lenders”), which Lenders constitute all Lenders under the Credit Agreement (as defined below), and CITIBANK, N.A., as administrative agent for the Lenders (in such capacity, the “Administrative Agent”).

W I T N E S S E T H:

WHEREAS, the Borrower, the other Loan Parties, the Lenders and the Administrative Agent are parties to that certain Credit Agreement dated as of October 12, 2023 (as amended by that certain First Amendment to Credit Agreement dated as of July 8, 2024, that certain Second Amendment to Credit Agreement dated as of August 11, 2025, that certain Third Amendment to Credit Agreement dated as of September 12, 2025, and as further amended, restated, amended and restated, supplemented or otherwise modified from time to time prior to the effectiveness of this Amendment, the “Existing Credit Agreement”, and as further amended, restated, amended and restated, supplemented or otherwise modified from time to time, the “Credit Agreement”), pursuant to which the Lenders committed to make certain loans and other financial accommodations to the Borrower upon the terms and conditions set forth therein;

WHEREAS, pursuant to Section 7.02(u) of the Credit Agreement, the Borrower is permitted to incur an unlimited amount of unsecured Convertible Notes subject to compliance with the conditions set forth therein, including, without limitation, that after giving effect to the incurrence of such Convertible Notes, the Consolidated Total Net Leverage Ratio determined on a Pro Forma Basis (without netting of any cash proceeds thereof) as of the end of the most recently ended Measurement Period shall not be greater than 4.00 to 1.00 (the “Convertible Note Incurrence Test”);

WHEREAS, the Borrower has informed the Administrative Agent and the Lenders that the Borrower intends to incur unsecured Convertible Notes on or about the date hereof in an aggregate original principal amount not to exceed $700,000,000.00 (the “2026 Convertible Note Transaction”), but that the Borrower will be unable to satisfy the Convertible Note Incurrence Test;

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WHEREAS, the Borrower has requested that the Administrative Agent and the Lenders consent to the 2026 Convertible Note Transaction notwithstanding the Borrower’s noncompliance with the Convertible Note Incurrence Test; and

WHEREAS, the Administrative Agent and the Lenders party hereto are willing to provide such consent on the terms and conditions contained in this Amendment.

NOW, THEREFORE, in consideration of the premises, the covenants and agreements contained herein, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, each Loan Party, the Lenders party hereto and the Administrative Agent do hereby agree that the Preamble and Recitals are incorporated into this Amendment in their entirety, and that capitalized terms used herein and not otherwise defined herein shall have the meanings given to such terms in the Credit Agreement and further agree as follows:

1. Acknowledgment of Obligations. The Borrower and each other Loan Party hereby acknowledge, confirm and agree that all credit extensions made under the Credit Agreement and the other Loan Documents prior to the date hereof, together with interest accrued and accruing thereon, and fees, costs, expenses and other charges owing by the Loan Parties to the Administrative Agent and Lenders under the Credit Agreement and the other Loan Documents, are unconditionally owing by the Loan Parties to the Administrative Agent and Lenders, without offset, defense or counterclaim of any kind, nature or description whatsoever except as such enforceability may be limited by bankruptcy, insolvency, and other similar laws affecting the rights of creditors generally or by general principles of equity (whether enforcement is sought by proceedings in equity or at law).

2. Consent. Subject to the terms and conditions of this Amendment (including without limitation the fulfillment of the conditions to effectiveness specified in Section 4 below), the Administrative Agent and the undersigned Lenders hereby consent to the 2026 Convertible Note Transaction notwithstanding the Borrower’s noncompliance with the Convertible Note Incurrence Test so long as the remaining conditions set forth in Section 7.02(u) of the Credit Agreement are satisfied with respect to the 2026 Convertible Note Transaction. The aforesaid consent relates solely to the Convertible Note Incurrence Test and the 2026 Convertible Note Transaction and nothing in this Amendment is intended or shall be construed to be (i) a consent to any other transaction or request by the Borrower or any other Loan Party or (ii) a waiver by the Administrative Agent or any Lender of any Default or Event of Default which may currently exist or hereafter occur.

3. Amendments to Existing Credit Agreement. Subject to the terms and conditions of this Amendment, including without limitation the fulfillment of the conditions to effectiveness specified in Section 4 below:

(a) Section 7.11(a) of the Existing Credit Agreement is hereby amended and restated in its entirety to read as follows:

Minimum Consolidated EBITDA. Permit Consolidated EBITDA for the most recently ended four (4) consecutive fiscal quarter period as of the end of any Measurement Period ending as of the end of any fiscal quarter of the Borrower to be less than (i) from the Closing Date to (and including) the fiscal quarter ended June 30, 2025, $45,000,000, (ii) from the fiscal quarter ended September 30, 2025 to (and including) the fiscal quarter ending March 31, 2026, $55,000,000, (iii) from the fiscal quarter ending June 30, 2026 to (and including) the fiscal quarter ending March 31, 2027, $100,000,000, and (iv) from and after the fiscal quarter ending June 30, 2027, $150,000,000.

(b) Exhibit C to the Existing Credit Agreement (Form of Compliance Certificate) is hereby amended and restated in its entirety to read as set forth on Exhibit A attached hereto.

4. Amendment Effectiveness; Conditions Precedent. The effectiveness of this Amendment (including, without limitation, the consent in Section 2 and the amendments in Section 3 above) is subject to the receipt by the Administrative Agent from each party hereto of counterparts of this Amendment executed by a Responsible Officer of each Loan Party and a duly authorized officer of each Lender and the Administrative Agent (the date of such satisfaction, the “Amendment Effective Date”).

Without limiting the generality of the provisions of Section 9.03(c) of the Credit Agreement, for purposes of determining compliance with the conditions specified in this Section 4, each Lender that has signed this Amendment shall be deemed to have consented to, approved or accepted or to be satisfied with, each document or other matter required thereunder to be consented to or approved by or acceptable or satisfactory to a Lender unless the Administrative Agent shall have received notice from such Lender prior to the proposed Amendment Effective Date specifying its objection thereto.

5. Representations and Warranties. The Borrower and each other Loan Party hereby represents and warrants to the Administrative Agent and the Lenders as follows:

(a) Representations and Warranties. On and as of the date hereof, after giving effect to this Amendment, (i) the representations and warranties of the Borrower and each other Loan Party contained in Article II or Article V of the Credit Agreement or any other Loan Document, or which are contained in any document furnished at any time under or in connection therewith, are true and correct in all material respects (except, if a qualifier relating to materiality, Material Adverse Effect or a similar concept applies, such representation or warranty is true and correct in all respects), except to the extent that such representations and warranties specifically refer to an earlier date, in which case they are true and correct in all material respects (except, if a qualifier relating to materiality, Material Adverse Effect or a similar concept applies, such representation or warranty is true and correct in all respects) as of such earlier date, and except that for purposes hereof, the representations and warranties contained in Sections 5.05(a) and (c), and Section 5.05(b) of the Credit Agreement shall be deemed to refer to the most recent statements furnished pursuant to Sections 6.01(a) and Section 6.01(b) of the Credit Agreement, respectively, and (ii) no Default or Event of Default has occurred and is continuing.

(b) Authorization; No Contravention. The execution and delivery of this Amendment (and any other Loan Documents executed and delivered in connection herewith) and performance by each Loan Party of this Amendment, the Credit Agreement and each other Loan Document executed and delivered in connection herewith to which such Person is a party have been duly authorized by all necessary corporate or other organizational action, and do not and will not (i) contravene the terms of any of such Person’s Organization Documents; (ii) conflict with or result in any breach or contravention of in any material respect, or the creation of (or the requirement to create) any Lien under, or require any payment to be made under (x) any material Contractual Obligation to which such Person is a party or affecting such Person or the properties of such Person or any of its Subsidiaries or (y) any order, injunction, writ or decree of any Governmental Authority or any arbitral award to which such Person or its property is subject; or (iii) violate any Applicable Law in any material respect.

(c) Binding Effect. This Amendment has been, and each other Loan Document executed and delivered in connection herewith, when delivered, will have been, duly executed and delivered by each Loan Party that is party thereto. This Amendment and the Credit Agreement constitute, and each other Loan Document executed and delivered in connection herewith when so delivered will constitute, a legal, valid and binding obligation of such Loan Party, enforceable against each Loan Party that is party thereto in accordance with its terms, subject to applicable bankruptcy, insolvency, reorganization, moratorium or other laws affecting creditors’ rights generally and subject to general principles of equity.

6. Provisions of General Application.

(a) Effect of this Amendment. Except as expressly set forth herein, no other changes or modifications to the Credit Agreement or other Loan Documents, waivers by the Administrative Agent or Lenders of any Default or Event of Default or consent of the Administrative Agent or Lenders to any other transaction are intended or implied hereby, and in all other respects the Loan Documents are hereby specifically ratified, restated and confirmed by the Borrower and the other Loan Parties as of the effective date hereof. No novation shall result from this Amendment. To the extent of conflict between the terms of this Amendment and the other Loan Documents, the terms of this Amendment shall control.

(b) Compliance. The Administrative Agent and the Lenders hereby notify the Loan Parties that, effective from and after the date of this Amendment, the Administrative Agent and the Lenders intend to enforce all of the provisions of the Loan Documents and that the Administrative Agent and the Lenders expect that the Loan Parties will comply in all respects with the terms of the Loan Documents from and after this date.

(c) Costs and Expenses. The Loan Parties shall pay all reasonable and documented out-of-pocket expenses incurred by the Administrative Agent and its Affiliates (including, but not limited to, the reasonable and documented fees, charges and disbursements of outside counsel for the Administrative Agent and its Affiliates (limited to one primary counsel to the Administrative Agent and its Affiliates (taken as a whole), and, if reasonably necessary, one additional local counsel in any relevant jurisdiction) in connection with the preparation, negotiation, execution, delivery and administration of this Amendment (whether or not the transactions contemplated hereby shall be consummated) and any agreements delivered in connection with the transactions contemplated hereby, all in accordance with the terms and conditions set forth in Section 11.04 of the Credit Agreement.

(d) Binding Effect. This Amendment shall be binding upon and inure to the benefit of the parties hereto and their respective successor and assigns to the extent such assignees are permitted assignees as provided in Section 11.06 of the Credit Agreement.

(e) Survival of Representations and Warranties. All representations and warranties made hereunder and in any other document delivered pursuant hereto or in connection herewith shall survive the execution and delivery hereof and thereof. Such representations and warranties have been or will be relied upon by the Administrative Agent and each Lender, regardless of any investigation made by the Administrative Agent or any Lender or on their behalf.

(f) Severability. If any provision of this Amendment is held to be illegal, invalid or unenforceable, (i) the legality, validity and enforceability of the remaining provisions of this Amendment shall not be affected or impaired thereby and (ii) the parties shall endeavor in good faith negotiations to replace the illegal, invalid or unenforceable provisions with valid provisions the economic effect of which comes as close as possible to that of the illegal, invalid or unenforceable provisions. The invalidity of a provision in a particular jurisdiction shall not invalidate or render unenforceable such provision in any other jurisdiction.

(g) Reviewed by Attorneys. The Borrower and each other Loan Party represents and warrants to the Administrative Agent and the Lenders that it (i) understands fully the terms of this Amendment and the consequences of the execution and delivery of this Amendment, (ii) has been afforded an opportunity to have this Amendment reviewed by, and to discuss this Amendment and document executed in connection herewith with, such attorneys and other persons as such Loan Party may wish, and (iii) has entered into this Amendment and executed and delivered all documents in connection herewith of its own free will and accord and without threat, duress or other coercion of any kind by any Person. The parties hereto acknowledge and agree that neither this Amendment nor the other documents executed pursuant hereto shall be construed more favorably in favor of one than the other based upon which party drafted the same, it being acknowledged that all parties hereto contributed substantially to the negotiation and preparation of this Amendment and the other documents executed pursuant hereto or in connection herewith.

(h) Governing Law; Submission to Jurisdiction; Waiver of Venue; Service of Process; Waiver of Jury Trial. Sections 11.14 and 11.15 of the Credit Agreement are hereby incorporated by reference as if fully set forth herein mutatis mutandis.

(i) Counterparts. This Amendment may be executed in any number of counterparts with the same effect as if all signatories had signed the same document. All counterparts must be construed together to constitute one and the same instrument. This Amendment may be signed and transmitted by facsimile, portable document format (PDF), or other electronic means, and shall have the same effect as manually-signed originals and shall be binding on the Loan Parties, the Administrative Agent and the Lenders. Notwithstanding the foregoing, Administrative Agent may, in its sole and exclusive discretion, also require delivery of this Amendment, and any amendments or waivers hereto, with an original signature for its records. Without limiting the foregoing provisions of this Section 6(i), the provisions of Section 11.18 of the Credit Agreement shall be applicable to this Amendment.

(j) Entire Agreement. This Amendment, together with all the Loan Documents executed and delivered in connection herewith (collectively, the “Relevant Documents”), sets forth the entire understanding and agreement of the parties hereto in relation to the subject matter hereof and supersedes any prior negotiations and agreements among the parties relating to such subject matter. No promise, condition, representation or warranty, express or implied, not set forth in the Relevant Documents shall bind any party hereto, and no such party has relied on any such promise, condition, representation or warranty. Each of the parties hereto acknowledges that, except as otherwise expressly stated in the Relevant Documents, no representations, warranties or commitments, express or implied, have been made by any party to the other with respect to the subject matter hereof. None of the terms or conditions of this Amendment may be changed, modified, waived or canceled orally or otherwise, except in writing and in accordance with Section 11.01 of the Credit Agreement.

(k) Austrian Capital Maintenance Rules. Any indemnity, obligation and/or liability assumed and/or provided by APEIRON Biologics GmbH, an Austrian limited liability company (Gesellschaft mit beschränkter Haftung) registered with the Austrian companies register under the number FN 242223 k and with the registered address Campus-Vienna-Biocenter 5, 1030 Vienna, Austria (“APEIRON”) under this Amendment shall be provided and/or assumed subject to, mutatis mutandis, the same limitations as set out in Section 6 of that certain Joinder Agreement, dated as of December 20, 2024, by and among APEIRON, the Borrower and the Administrative Agent.

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IN WITNESS WHEREOF, the parties have caused this Amendment to be duly executed by their respective officers thereunto duly authorized, as of the date first above written.

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[SIGNATURE PAGE TO CONSENT AGREEMENT – LIGAND PHARMACEUTICALS INCORPORATED]

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EXHIBIT A

[Intentionally omitted]

Exhibit 99.1

Ligand Announces Proposed Offering of $550 Million of Convertible Senior Notes Due 2031

JUPITER, Fla., June 22, 2026 (GLOBE NEWSWIRE) — Ligand Pharmaceuticals Incorporated (Nasdaq: LGND) (“Ligand”) announced today its intention to offer $550.0 million aggregate principal amount of convertible senior notes due 2031 (the “notes”) in a private placement (the “offering”) to persons reasonably believed to be qualified institutional buyers pursuant to Rule 144A under the Securities Act of 1933, as amended (the “Securities Act”), subject to market conditions and other factors. Ligand also expects to grant to the initial purchasers of the notes (the “initial purchasers”) a 13-day option to purchase up to an additional $82.5 million aggregate principal amount of notes.

Key Elements of the Transaction

The notes will be general unsecured, senior obligations of Ligand and will accrue interest payable semiannually in arrears on March 15 and September 15 of each year, beginning on March 15, 2027. The notes will mature on September 15, 2031, unless earlier converted, redeemed or repurchased. Upon conversion of the notes, Ligand will pay cash up to the aggregate principal amount of the notes to be converted and pay or deliver, as the case may be, cash, shares of Ligand’s common stock or a combination of cash and shares of Ligand’s common stock, at Ligand’s election, in respect of the remainder, if any, of Ligand’s conversion obligation in excess of the aggregate principal amount of the notes being converted. The interest rate, initial conversion rate, redemption or repurchase rights and other terms of the notes will be determined at the time of pricing of the offering.

Use of Proceeds

Ligand expects to use a portion of the net proceeds from the offering to pay the cost of the convertible note hedge transactions described below (after such cost is partially offset by the proceeds to Ligand from the sale of the warrants in the warrant transactions described below). In addition, Ligand expects to use up to $75 million of the net proceeds from the offering to repurchase shares of its common stock from certain purchasers of the notes in privately negotiated transactions, as described below. Ligand intends to use the remaining net proceeds from the offering for general corporate purposes including investing in complementary businesses, companies, products and technologies, although Ligand has no present commitments or agreements to do so beyond its previously announced agreement to acquire Xoma Royalty Corporation. If the initial purchasers exercise their option to purchase additional notes, Ligand expects to sell additional warrants to the option counterparties and use a portion of the net proceeds from the sale of the additional notes, together with the proceeds from the sale of the additional warrants, to enter into additional convertible note hedge transactions and the remaining net proceeds for general corporate purposes.

Convertible Note Hedge Transactions

In connection with the pricing of the notes, Ligand expects to enter into convertible note hedge transactions (the “convertible note hedge transactions”) with one or more of the initial purchasers or their respective affiliates and/or other financial institutions (the “option counterparties”). Ligand also expects to enter into warrant transactions (the “warrant transactions”) with the option counterparties, pursuant to which Ligand will issue warrants to purchase common stock (the “warrants”) to such option counterparties. The convertible note hedge transactions are expected generally to reduce the potential dilution to Ligand’s common stock upon any conversion of notes and/or offset any cash payments Ligand is required to make in excess of the principal amount of converted notes, as the case may be. However, the warrant transactions could separately have a dilutive effect on Ligand’s common stock to the extent that the market price per share of common stock exceeds the strike price of the warrants. If the initial purchasers exercise their option to purchase additional notes, Ligand expects to enter into additional convertible note hedge transactions and additional warrant transactions with the option counterparties.

In connection with establishing their initial hedges of the convertible note hedge transactions and the warrant transactions, Ligand expects the option counterparties or their respective affiliates to enter into various derivative transactions with respect to Ligand’s common stock and/or purchase shares of Ligand’s common stock concurrently with or shortly after the pricing of the notes. This activity could increase (or reduce the size of any decrease in) the market price of Ligand’s common stock or the notes at that time.

The option counterparties or their respective affiliates may modify their hedge positions by entering into or unwinding various derivatives with respect to Ligand’s common stock and/or purchasing or selling shares of Ligand’s common stock or other securities of Ligand in secondary market transactions following the pricing of the notes and prior to the maturity of the notes (and are likely to do so in connection with any conversion, redemption or repurchase of the notes). This activity could also cause or avoid an increase or a decrease in the market price of Ligand’s common stock or the notes, which could affect a holder’s ability to convert its notes and, to the extent the activity occurs during any observation period related to a conversion of notes, it could affect the number of shares of Ligand’s common stock, if any, and value of the consideration, if any, that a holder will receive upon conversion of its notes.

Share Repurchases

In addition, Ligand expects to use up to $75 million of the net proceeds from the offering to repurchase shares of its common stock from certain purchasers of the notes in privately negotiated transactions effected through one of the initial purchasers or an affiliate thereof concurrently with the pricing of the notes. The price per share of Ligand’s common stock repurchased in such transactions is expected to equal the last reported price per share of Ligand’s common stock as of the date of the pricing of the notes. These repurchases could increase (or reduce the size of any decrease in) the market price of Ligand’s common stock prior to, concurrently with or shortly after the pricing of the notes, and could result in a higher effective conversion price for the notes. Ligand cannot predict the magnitude of such market activity or the overall effect it will have on the market price of the notes and/or the market price of Ligand’s common stock.

The notes and the warrants will only be offered to persons reasonably believed to be qualified institutional buyers pursuant to Rule 144A under the Securities Act. The notes, the warrants, the shares of common stock into which the notes are convertible and the shares of common stock issuable upon exercise of the warrants have not been, and will not be, registered under the Securities Act or the securities laws of any other jurisdiction, and unless so registered, may not be offered or sold in the United States or to, or for the account or benefit of, U.S. persons, absent registration or an applicable exemption from, or in a transaction not subject to, the registration requirements of the Securities Act and other applicable securities laws.

This press release is neither an offer to sell nor a solicitation of an offer to buy any securities, nor shall it constitute an offer to sell, solicitation of an offer to buy or sale of any securities in any state or jurisdiction in which such offer, solicitation or sale would be unlawful prior to the registration or qualification under the securities laws of any such state or jurisdiction.

Forward-Looking Statements

This press release contains “forward-looking” statements, which are subject to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. Forward-looking statements are often identified by the use of words such as, but not limited to, “anticipate,” “believe,” “can,” “continue,” “could,” “estimate,” “expect,” “predict,” “intend,” “may,” “might,” “plan,” “project,” “potential,” “seek,” “should,” “target,” “will,” “would” and similar expressions or variations intended to identify forward-looking statements. All statements other than statements of historical facts contained in this press release, including statements regarding whether Ligand will offer the notes or the warrants or consummate the offering, the convertible note hedge transactions or the warrant transactions on the expected terms, or at all; the anticipated use of the net proceeds of the offering and the warrant transactions; and the potential effects of entering into the hedge transactions and the warrant transactions are forward-looking statements. Actual results may differ materially from those indicated by such forward-looking statements as a result of various important risk factors that are described more fully in Ligand’s reports and other documents filed with the Securities and Exchange Commission (the “SEC”), including its Annual Report on Form 10-K for the year ended December 31, 2025 and other flings that Ligand makes from time to time with the SEC, which are available on the SEC’s website at www.sec.gov, and could cause actual results to vary from expectations. All information provided in this press release is as of the date hereof, and Ligand undertakes no duty to update or revise this information, whether as a result of new information, new developments or otherwise, except as required by law, are forward-looking statements. These statements are not guarantees of future performance but are based on management’s expectations as of the date of this press release and assumptions that are inherently subject to uncertainties, risks and changes in circumstances that are difficult to predict. Forward-looking statements involve known and unknown risks, uncertainties and other factors that may cause actual results, performance or achievements to be materially different from any future results, performance or achievements.

About Ligand Pharmaceuticals

Ligand is a leading royalty aggregator, partnering with biopharmaceutical companies to finance and advance late-stage clinical development programs. Ligand owns and manages one of the largest and most diversified portfolios of biopharmaceutical royalties in the industry, with economic interests in more than 100 development and commercial-stage assets. Ligand funds high-value programs in exchange for long-term economic interests, aligning capital with clinical and commercial success. Ligand’s royalty portfolio is designed to deliver consistent and predictable revenue streams across a broad range of therapeutic assets. Ligand also licenses its proprietary technologies, Captisol^® and NITRICIL^™, to support drug development and formulation across its global partner network.

Contacts

Investors:

Melanie Herman

[email protected]

(858) 550-7761

Media:

Kellie Walsh

[email protected]

(914) 315-6072