ULTRAGENYX PHARMACEUTICAL INC. (Name of Registrant As Specified in Its Charter)

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Definitive Proxy Statement ☐ Definitive Additional Materials ☐ Soliciting Material under §240.14a-12 ULTRAGENYX PHARMACEUTICAL INC. (Name of Registrant as Specified In Its Charter) N/A (Name of Person(s) Filing Proxy Statement, if Other Than The Registrant) Payment of Filing Fee (Check the appropriate box): ☒ No fee required. ☐ Fee computed on table below per Exchange Act Rules 14a-6(i)(1) and 0-11. (1) Title of each class of securities to which transaction applies: (2) Aggregate number of securities to which transaction applies: (3) Per unit price or other underlying value of transaction computed pursuant to Exchange Act Rule 0-11 (set forth the amount on which the filing fee is calculated and state how it was determined): (4) Proposed maximum aggregate value of transaction: (5) Total fee paid: ☐ Fee paid previously with preliminary materials. ☐ Check box if any part of the fee is offset as provided by Exchange Act Rule 0-11(a)(2) and identify the filing for which the offsetting fee was paid previously. Identify the previous filing by registration statement number, or the Form or Schedule and the date of its filing. (1) Amount Previously Paid: (2) Form, Schedule or Registration Statement No.: (3) Filing Party: (4) Date Filed: Table of Contents 60 Leveroni Court Novato, California 94949 NOTICE OF ANNUAL MEETING OF STOCKHOLDERS To Be Held on June 26, 2020 at 8:00 a.m. Pacific Time Dear Stockholder: You are cordially invited to attend the Annual Meeting of Stockholders of Ultragenyx Pharmaceutical Inc., a Delaware corporation (the “ Company ”), which will be held on June 26, 2020, at 8:00 a.m. Pacific Time virtually via the Internet at www.virtualshareholdermeeting.com/RARE20 (the “ Annual Meeting ”). Instructions on how to participate in the Annual Meeting and demonstrate proof of stock ownership are posted at www.virtualshareholdermeeting.com/RARE20 . The webcast of the Annual Meeting will be archived for one year after the date of the Annual Meeting at www.virtualshareholdermeeting.com/RARE20 . Only stockholders who held stock at the close of business on the record date, April 27, 2020, may vote at the Annual Meeting, including any adjournment or postponement thereof. At the Annual Meeting, you will be asked to consider and vote upon: (1) the election of the three directors named in the Proxy Statement as Class I directors; (2) the ratification of the selection of Ernst & Young LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2020; (3) an advisory (non-binding) resolution to approve the compensation of our named executive officers; and (4) any other business that may properly come before the Annual Meeting or any adjournment or postponement thereof. No other items of business are expected to be considered, and no other director nominees will be entertained, at the Annual Meeting. The accompanying Proxy Statement more fully describes the details of the business to be conducted at the Annual Meeting. Proposal No. 1 relates solely to the election of the three directors nominated by the Board of Directors. After careful consideration, our Board of Directors has unanimously approved the proposals and recommends that you vote FOR each of the three director nominees and FOR each proposal described in the Proxy Statement. In accordance with Delaware law, a list of stockholders entitled to vote at the Annual Meeting will be available in electronic form during the Annual Meeting at the following URL: www.virtualshareholdermeeting.com/RARE20 and will be accessible during normal business hours for ten days prior to the meeting at our principal place of business, 60 Leveroni Court, Novato, California 94949. We are pleased to make use of the Securities and Exchange Commission rules that allow companies to furnish proxy materials to their stockholders via the Internet. We believe the ability to deliver proxy materials electronically allows us to provide our stockholders with the information they need, while lowering the costs of delivery and reducing the environmental impact from the distribution of our Annual Meeting materials. We look forward to speaking with you at the Annual Meeting. Sincerely, Emil D. Kakkis, M.D., Ph.D. President and Chief Executive Officer April 29, 2020 WHETHER OR NOT YOU EXPECT TO ATTEND THE ANNUAL MEETING, PLEASE VOTE VIA THE INTERNET AS INSTRUCTED IN THE NOTICE OF INTERNET AVAILABILITY OR, IF YOU REQUESTED AND RECEIVED A PRINTED COPY OF THE PROXY STATEMENT, COMPLETE, DATE, SIGN, AND RETURN THE ENCLOSED PROXY CARD USING THE ENCLOSED RETURN ENVELOPE, AS PROMPTLY AS POSSIBLE SO THAT YOUR SHARES MAY BE REPRESENTED AT THE ANNUAL MEETING. YOU MAY ALSO VOTE THROUGH OUR VIRTUAL WEB CONFERENCE IF YOU ATTEND THE ANNUAL MEETING. IMPORTANT NOTICE REGARDING THE AVAILABILITY OF PROXY MATERIALS FOR THE ANNUAL MEETING OF STOCKHOLDERS TO BE HELD ON JUNE 26, 2020: The Proxy Statement and Annual Report on Form 10-K for the year ended December 31, 2019 are available at www.proxyvote.com. Table of Contents TABLE OF CONTENTS GENERAL INFORMATION 1 Shares Outstanding and Voting Rights 1 Virtual Meeting 3 PROPOSAL NO. 1 – ELECTION OF CLASS I DIRECTORS 4 Nomination of Directors 4 Nominees and Incumbent Directors 6 Class I Directors Nominated for Election 6 Class II Directors Continuing in Office Until 2021 7 Class III Directors Continuing in Office Until 2022 8 Vote Required 9 Director Resignation Policy 9 PROPOSAL NO. 2 – RATIFICATION OF THE SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM 10 Fees for Independent Registered Public Accounting Firm 11 Vote Required 11 REPORT OF THE AUDIT COMMITTEE 12 PROPOSAL NO. 3 – ADVISORY (NON-BINDING) VOTE TO APPROVE THE COMPENSATION OF OUR NAMED EXECUTIVE OFFICERS 13 Background 13 Vote Required 13 CORPORATE GOVERNANCE 14 Director Independence 14 Global Code of Conduct 14 Stockholder Communications 14 BOARD OF DIRECTORS AND COMMITTEES 14 Board Leadership Structure and Risk Oversight 15 Board Committees 15 Compensation Committee Interlocks and Insider Participation 17 EXECUTIVE OFFICERS 18 CERTAIN RELATIONSHIPS AND RELATED-PERSON TRANSACTIONS 19 Related-Person Transactions 19 Procedures for Related-Person Transactions 20 DELINQUENT SECTION 16(A) BENEFICIAL OWNERSHIP REPORTS 21 SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT 22 EXECUTIVE COMPENSATION 26 Compensation Discussion and Analysis 26 Executive Summary 26 Stockholder Outreach 28 Compensation Philosophy and Objectives 29 Roles in Determining Compensation 30 Defining and Comparing Compensation to Market Benchmarks 31 Annual Performance Reviews 32 Base Salary 32 Annual Bonus 33 Table of Contents Equity Compensation 37 Fiscal 2020 Compensation 39 Employee Benefit Program 40 Tax and Accounting Considerations 41 Allocation of Compensation 41 Timing of Compensation Actions 41 Clawback Policy 41 Minimum Stock Ownership Requirements 42 Risk Management and Mitigation 42 Compensation Committee Report 42 Summary Compensation Table 43 Narrative Disclosure to Summary Compensation Table 44 Grants of Plan-Based Awards 48 Outstanding Equity Awards at December 31, 2019 49 Option Exercises and Stock Vested 50 Pension Benefits 50 Nonqualified Deferred Compensation 51 Potential Payments Upon Termination or Change of Control 51 EQUITY COMPENSATION PLAN INFORMATION 53 DIRECTOR COMPENSATION 53 CEO PAY RATIO 55 OTHER BUSINESS 55 STOCKHOLDER PROPOSALS 55 DELIVERY OF PROXY MATERIALS 56 Table of Contents 60 Leveroni Court Novato, California 94949 PROXY STATEMENT FOR 2020 ANNUAL MEETING OF STOCKHOLDERS TO BE HELD ON JUNE 26, 2020 at 8:00 a.m. Pacific Time GENERAL INFORMATION This Proxy Statement is furnished in connection with the solicitation of proxies by the Board of Directors (the “ Board ”) of Ultragenyx Pharmaceutical Inc. (“ Ultragenyx ” or the “ Company ”) for use at the Company’s 2020 Annual Meeting of Stockholders, to be held virtually via the Internet at www.virtualshareholdermeeting.com/RARE20 on June 26, 2020, at 8:00 a.m. Pacific Time (the “ Annual Meeting ”). The Notice Regarding the Availability of Proxy Materials (the “ Notice ”) containing instructions on how to access this Proxy Statement and our Annual Report on Form 10-K for the fiscal year ended December 31, 2019 (the “ Annual Report ”) is first being mailed on or about April 29, 2020 to all stockholders entitled to vote at the Annual Meeting. Pursuant to the rules promulgated by the Securities and Exchange Commission (the “ SEC ”), we have elected to provide access to our proxy materials primarily by notifying you of the availability of our proxy materials on the Internet, instead of mailing printed copies of those materials to stockholders. The Proxy Statement and Annual Report are available at www.ultragenyx.com in the “SEC Filings” subsection of the “Investors” tab. The Notice instructs you as to how you may access and review important information contained in the proxy materials. The Notice also instructs you on how you may submit your proxy via the Internet. If you receive a Notice by mail and would like to receive a printed copy of our proxy materials, you should follow the instructions for requesting such materials included in the Notice. For a proxy to be effective, it must be properly executed and received prior to the Annual Meeting. Each proxy properly tendered will, unless otherwise directed by the stockholder, be voted for each of the proposals set forth in this Proxy Statement and each of the three director nominees named in this Proxy Statement and at the discretion of the proxy holder(s) with regard to all other matters that may properly come before the Annual Meeting. We will pay all of the costs of soliciting proxies.

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