Abu Dhabi  Beijing  Brussels  Century City  Dallas  Denver  Dubai  Frankfurt  Hong Kong  Houston  London  Los Angeles Munich  New York  Orange County  Palo Alto  Paris  San Francisco  Singapore  Washington, D.C. Exhibit 5.1 February 28, 2024 Arrowhead Pharmaceuticals, Inc. 177 E. Colorado Blvd, Suite 700 Pasadena, CA 91105 Re: Arrowhead Pharmaceuticals, Inc. Registration Statement on Form S-8 Ladies and Gentlemen: We have examined the Registration Statement on Form S-8 (the “Registration Statement”) of Arrowhead Pharmaceuticals, Inc., a Delaware corporation (the “Company”), to be filed with the Securities and Exchange Commission (the “Commission”) pursuant to the Securities Act of 1933, as amended (the “Securities Act”), in connection with the offering by the Company of up to 555,300 shares of the Company’s Common Stock, par value $0.001 per share (the “Shares”). The Shares subject to the Registration Statement are to be issued under the Arrowhead Pharmaceuticals, Inc. Inducement Plan (the “Plan”) and include certain previously issued restricted stock unit awards granted at various dates from March 29, 2023 through December 28, 2023 to new employees as inducement awards in connection with the commencement of employment. We have examined the originals, or photostatic or certified copies, of such records of the Company and certificates of officers of the Company and of public officials and such other documents as we have deemed relevant and necessary as the basis for the opinions set forth below. In our examination, we have assumed the genuineness of all signatures, the legal capacity and competency of all natural persons, the authenticity of all documents submitted to us as originals and the conformity to original documents of all documents submitted to us as copies. We have also assumed that there are no agreements or understandings between or among the Company and any participants in the Plan that would expand, modify or otherwise affect the terms of the Plan or the respective rights or obligations of the participants thereunder. Finally, we have assumed the accuracy of all other information provided to us by the Company during the course of our investigations, on which we have relied in issuing the opinion expressed below. Based upon the foregoing examination and in reliance thereon, and subject to the qualifications, assumptions and limitations stated herein and in reliance on the statements of fact contained in the documents that we have examined, we are of the opinion that the

Arrowhead Pharmaceuticals, Inc. February 28, 2024 Page 2 Shares, when issued and sold in accordance with the terms set forth in the Plan and against payment therefor, and when the Registration Statement has become effective under the Securities Act, will be validly issued, fully paid and non-assessable. We render no opinion herein as to matters involving the laws of any jurisdiction other than the Delaware General Corporation Law (the “DGCL”). We are not admitted to practice in the State of Delaware; however, we are generally familiar with the DGCL as currently in effect and have made such inquiries as we consider necessary to render the opinions above. This opinion is limited to the effect of the current state of the DGCL and the facts as they currently exist. We assume no obligation to revise or supplement this opinion in the event of future changes in such law or the interpretations thereof or such facts. We consent to the filing of this opinion as an exhibit to the Registration Statement. In giving these consents, we do not thereby admit that we are within the category of persons whose consent is required under Section 7 of the Securities Act or the Rules and Regulations of the Commission. Very truly yours, /s/ Gibson, Dunn & Crutcher LLP