Exhibit 5.1

July 21, 2015

Ultragenyx Pharmaceutical Inc.

60 Leveroni Ct.

Novato, CA 94949

Ladies and Gentlemen:

We have examined the Registration Statement on Form S-3, File No. 333-201838 (the “Registration Statement”), of Ultragenyx Pharmaceutical 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”), and the prospectus supplement thereto dated July 15, 2015 (the “Prospectus Supplement”), in connection with the offering by the Company of up to 2,530,000 shares (including shares that may be sold upon exercise of the underwriters’ option to purchase additional shares from the Company) of the Company’s common stock, par value $0.001 per share, (the “Shares”).

In arriving at the opinion expressed below, we have examined originals, or copies certified or otherwise identified to our satisfaction as being true and complete copies of the originals, of specimen Common Stock certificate and such other documents, corporate records, certificates of officers of the Company and of public officials and other instruments as we have deemed necessary or advisable to enable us to render the opinions set forth below. In our examination, we have assumed without independent investigation 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.

Based upon the foregoing, and subject to the assumptions, exceptions, qualifications and limitations set forth herein, we are of the opinion that the Shares, when issued against payment therefor as set forth in the Registration Statement and the Prospectus Supplement thereto, will be validly issued, fully paid and non-assessable.

We consent to the filing of this opinion as an exhibit to the Registration Statement, and we further consent to the use of our name under the caption “Legal Matters” in the Registration Statement and the Prospectus Supplement. 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.

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July 21, 2015

Page 2

Very truly yours,

/s/ GIBSON DUNN & CRUTCHER LLP

GIBSON DUNN & CRUTCHER LLP