Gibson, Dunn & Crutcher LLP   555 Mission Street San Francisco, CA 94105-0921 Tel 415.393.8200 www.gibsondunn.com

EXHIBIT 5.1

March 29, 2019

Arrowhead Pharmaceuticals, Inc.

225 South Lake Avenue, Suite 1050

Pasadena, CA 91101

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”) 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: (a) 1,851,829 shares (the “Stock Plan Shares”) of the Company’s common stock, par value $0.001 per share (the “Common Stock”), issuable to eligible individuals under the Company’s 2013 Incentive Plan (the “Stock Plan”) and (b) 350,000 shares (the “Option Shares”) of Common Stock issuable pursuant to the Company’s Form of Stock Option Grant Inducement Award (the “Option Agreement”) and (c) 2,000 shares (the “RSU Shares” and together with the Stock Plan Shares and the Options Shares, the “Shares”) of Common Stock issuable pursuant to the Company’s Form of Restricted Stock Unit Inducement Award (the “RSU Agreement” and together with the Stock Plan and the Option Agreement, the “Governing Documents”).

In arriving at the opinions expressed below, we have examined the Governing Documents and 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. We have also made such other investigations as we have deemed relevant and necessary or appropriate in connection with the opinion hereinafter set forth. 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 Governing Documents that would expand, modify or otherwise affect the terms of the Governing Documents 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.

Beijing • Brussels • Century City • Dallas • Denver • Dubai • Hong Kong • London • Los Angeles • Munich

New York • Orange County • Palo Alto • Paris • San Francisco • São Paolo • Singapore • Washington, D.C.

Arrowhead Pharmaceuticals, Inc.

March 29, 2019

Page 2

Based upon the foregoing examination and in reliance thereon, and subject to the assumptions stated and in reliance on statements of fact contained in the documents that we have examined, we are of the opinion that the Shares issuable under the Governing Documents, when issued and sold in accordance with the terms of the respective Governing Documents 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 law 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 this consent, 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