UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of Earliest Event Reported): July 15, 2015

Ultragenyx Pharmaceutical Inc.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (415) 483-8800

Not Applicable

Former name or former address, if changed since last report

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

On July 15, 2015, Ultragenyx Pharmaceutical Inc. (“we,” “Ultragenyx” or the “Company”) entered into an underwriting agreement (the “Underwriting Agreement”) with Morgan Stanley & Co. LLC, J.P. Morgan Securities LLC and Cowen and Company, LLC, as representatives of the several underwriters (the “Underwriters”), pursuant to which we agreed to issue and sell an aggregate of 2,530,000 shares, including 330,000 shares to be sold pursuant to the exercise by the Underwriters of the option we granted the Underwriters to purchase such shares, (the “Shares”) of our common stock, par value $0.001 per share (the “Common Stock”) to the Underwriters (the “Offering”). The Shares will be sold at a public offering price of $120.00 per Share, and will be purchased by the Underwriters from us at a price of $113.40 per Share.

We estimate that net proceeds we will receive from the Offering will be approximately $286.6 million, after deducting the Underwriters’ discounts and commissions and estimated offering expenses payable by us.

The Offering is being made under a prospectus supplement and related prospectus filed with the Securities and Exchange Commission pursuant to the Company’s automatically effective shelf registration statement on Form S-3 (Registration No. 333-201838). The Offering was not registered under any state blue sky laws.

The Offering closed on July 21, 2015. In the Underwriting Agreement, the Company agrees to indemnify the Underwriters against certain liabilities, including liabilities under the Securities Act of 1933, as amended, or to contribute to payments that the Underwriters may be required to make because of such liabilities.

A copy of the Underwriting Agreement is attached as Exhibit 1.1 hereto and is incorporated herein by reference. The foregoing descriptions of the Underwriting Agreement do not purport to be complete and are qualified in their entirety by reference to such exhibits.

A copy of the opinion of Gibson, Dunn & Crutcher LLP relating to the validity of the securities issued in the Offering is filed herewith as Exhibit 5.1.

(d) Exhibits

* * *

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

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Exhibit Index

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