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SCHEDULE 13D/A 0001104659-23-065376 0001472322 XXXXXXXX LIVE 3 Common Stock, par value $0.0001 per share 06/06/2025 false 0001385818 054754858 AYTU BIOPHARMA, INC 7900 East Union Avenue, Suite 920 Denver CO 80237 Taki Vasilakis 203-308-4440 130 Main St., 2nd Floor New Canaan CT 06840 0001472322 N Nantahala Capital Management, LLC AF N MA 0.00 1086812.00 0.00 1086812.00 1086812.00 N 14.4 IA OO 0001775952 N Harkey Wilmot B. AF N X1 0.00 1086812.00 0.00 1086812.00 1086812.00 N 14.4 IN 0001775831 N Mack Daniel AF N X1 0.00 1086812.00 0.00 1086812.00 1086812.00 N 14.4 IN Common Stock, par value $0.0001 per share AYTU BIOPHARMA, INC 7900 East Union Avenue, Suite 920 Denver CO 80237 This Amendment No. 3 ("Amendment No. 3") amends and supplements the Schedule 13D filed with the Securities and Exchange Commission on behalf of Nantahala Capital Management, LLC, a Massachusetts limited liability company ("Nantahala"), and Messrs. Wilmot B. Harkey and Daniel Mack, the principals of Nantahala (collectively, the "Reporting Persons") on May 26, 2023 (the "Original Schedule 13D"), relating to Common Stock, par value $0.0001 per share (the "Common Stock"), of Aytu BioPharma, Inc. a Delaware corporation (the "Issuer") as previously amended by the Reporting Persons on June 13, 2023 and June 18, 2024. Capitalized terms used but not defined in this Amendment have the meanings set forth in the Original Schedule 13D as previously amended. Except as specifically provided herein, this Amendment does not modify any of the information reported in the Original Schedule 13D as previously amended. This Schedule 13D relates to Common Stock of the Issuer purchased by Nantahala through the accounts of certain private funds and managed accounts (collectively, the "Nantahala Investors"). Nantahala serves as the investment adviser to the Nantahala Investors and may direct the vote and dispose of the shares of Common Stock held by the Nantahala Investors. As the principals of Nantahala, Mr. Harkey and Mr. Mack may direct the vote and disposition of the shares of Common Stock held by the Nantahala Investors. Item 3 is amended by the addition of the following: The disclosure set forth in Item 4 to this Amendment is incorporated herein by reference. Item 4 is amended by the addition of the following: On June 6, 2025, the Reporting Persons caused the Nantahala Investors to purchase prefunded warrants (the "June 2025 Prefunded Warrants") in an underwritten offering (the "June 2025 Offering") by the Issuer. Using cash on hand, the Nantahala Investors purchased June 2025 Prefunded Warrants exercisable, subject to the terms and conditions thereof, for 4,000,000 shares of Common Stock. The Nantahala Investors purchased the June 2025 Prefunded Warrants for $1.4999 per share of Common Stock represented by the June 2025 Prefunded Warrants. The June 2025 Prefunded Warrant may be exercised at any time by payment of cash in the amount of $0.0001 per share of Common Stock, or by customary cashless exercise, provided that the June 2025 Prefunded Warrants may not be exercised if the holder (together with its affiliates) would beneficially own in excess of 9.99% of the number of shares of Common Stock outstanding immediately after giving effect to the exercise (which limit may be increased (but not in excess of 19.99%) or decreased by the holder upon at least 61 days' prior notice from the holder to the Issuer). The June 2025 Prefunded Warrants do not expire except upon exercise in full. The Prefunded Warrants are described more fully in in the Issuer's Registration Statement under the Securities Act of 1933 filed with the SEC on Form S-1 on June 2, 2025, as subsequently amended. Item 5(a) is amended and restated as follows: See Items 11 and 13 of the cover pages. The percentage of the outstanding shares of Common Stock beneficially owned by the Reporting Persons reported herein is based on 7,536,830 shares of Common Stock outstanding immediately after the June 2025 Offering, as communicated to the Reporting Persons by the Issuer. Item 5(b) is amended and restated as follows: See Items 7, 8, 9 and 10 of the cover pages. Item 5(c) is amended by the addition of the following: Other than the transactions reported herein, if applicable, no Reporting Person or Other Officer has effected any transactions in the Common Stock of the Issuer in the prior sixty days. Item 5(d) is amended and restated as follows: The Nantahala Investors hold the shares of Common Stock reported herein, including more than 5% of the outstanding shares of Common Stock beneficially owned by the Reporting Persons but held by Blackwell Partners LLC - Series A. No person other than the Nantahala Investors is known to have the right to receive, or the power to direct the receipt of dividends from, or proceeds from the sale of, the Common Stock. Not applicable. Item 6 is amended by the addition of the following: The disclosure regarding the June 2025 Prefunded Warrants set forth above in Item 4 is hereby incorporated herein. The form of the June 2025 Prefunded Warrants was disclosed by the Issuer as Exhibit 4.13 to the Issuer's Registration Statement under the Securities Act of 1933, filed by the Issuer with the SEC on Form S-1 on June 2, 2025. Item 7 is amended by the addition of the following: Exhibit 99.6 Form of Prefunded Warrant (incorporated by reference to Exhibit 4.13 to Registration Statement on Form S-1, filed by the Issuer with the SEC on June 2, 2025). (https://www.sec.gov/Archives/edgar/data/1385818/000143774925019189/ex_825697.htm) Nantahala Capital Management, LLC /s/ Taki Vasilakis Taki Vasilakis, Chief Compliance Officer 06/09/2025 Harkey Wilmot B. /s/ Wilmot B. Harkey Wilmot B. Harkey 06/09/2025 Mack Daniel /s/ Daniel Mack Daniel Mack 06/09/2025