#1ultragenyx Corporate Presentation February 2024 Confidential and Proprietary#2Forward looking statements Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but not limited to, statements regarding our expectations and projections regarding our future operating results and financial performance, anticipated cost or expense reductions, plans with respect to commercializing our product and product candidates, our translational research program, expectations regarding our manufacturing capabilities, the expected timing of release of additional data for our product candidates, plans to initiate additional studies for product candidates and timing and design of these studies, plans regarding ongoing studies for existing programs, our liquidity position as of the most recent fiscal quarter end, expectations regarding the adequacy of clinical data to support marketing applications and approvals of product candidates, our intent to file, and potential timing and success of, marketing applications and other regulatory approvals, expectations regarding timing of receiving potential approval of product candidates, expectations regarding prevalence of patients, future regulatory interactions, and the value to be generated by our pipeline. Such forward-looking statements involve substantial risks and uncertainties that could cause our clinical development programs, future results, performance or achievements to differ significantly from those expressed or implied by the forward-looking statements. Such risks and uncertainties include, among others, our reliance on our third party partner, Kyowa Kirin Co., Ltd., for the supply of Crysvita, fluctuations in buying or distribution patterns from distributors and specialty pharmacies, the transition back to Kyowa Kirin of our exclusive rights to promote Crysvita in the United States and Canada and unexpected costs, delays, difficulties or adverse impact to revenue related to such transition, smaller than anticipated market opportunities for our products and product candidates, manufacturing risks, competition from other therapies or products, uncertainties related to insurance coverage and reimbursement status of our newly approved products, our evolving integrated commercial organization, uncertainties in the regulatory approval process and the timing of our regulatory filings, the uncertainties inherent in the clinical drug development process, including the potential for substantial delays and risk that earlier study results may not be predictive of future study results, risks related to adverse side effects, the ability for us to successfully develop our pipeline product candidates, our ability to achieve our projected development goals in the expected time frames, the potential for any license or collaboration agreement to be terminated, and other matters that could affect sufficiency of existing cash, cash equivalents and short-term investments to fund operations, the availability or commercial potential of our product and product candidates, and our ability to integrate acquired businesses, which are more fully described in our most recent Form 10-Q or Form 10-K under the caption "Risk Factors" and elsewhere in such reports. Any forward-looking statements made by us reflect our current views with respect to future events or to our future financial performance and involve known and unknown risks, uncertainties, and other factors that may cause our actual results, performance, or achievements to be materially different from any future results, performance, or achievements expressed or implied by these forward-looking statements. Accordingly, our actual results may materially differ from our current expectations, estimates, and projections. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Any forward-looking statements made by us in this presentation speak only as of the date of this presentation and represent our estimates and assumptions only as of the date of this presentation. Except as required by law, we assume no obligation, and we disclaim any intent, to update these statements to reflect actual results. This presentation concerns commercial products as well as discussion of investigational drugs that are under preclinical and/or clinical investigation and which have not yet been approved for marketing by the U.S. Food and Drug Administration (FDA). They are currently limited by Federal law to investigational use, and no representations are made as to their safety or effectiveness for the purposes for which they are being investigated. Ultragenyx, Mepsevii, Dojolvi, Pinnacle PCL and our logo are our trademarks. Any other trademarks appearing in these slides are the property of their respective holders. 2 Confidential and Proprietary ultragenyx#3Most productive rare disease company in the industry 4 products across 5 indications approved in 10 years ♥ Evkeeza CRYSVITA DOJOLVI burosumab Largest clinical pipeline in rare disease Mepsevii® 3 Confidential and Proprietary modes targeting 6 late-stage studies 4 cause of disease ultragenyx#4Product approvals since IPO exceed other successful, rare disease companies ultragenyx BioMarin Genzyme Years from IPO to 1st approval^ # of approvals^ 10y post-IPO # of approvals^ 15y post-IPO 8-12* 3 53 2 2 5320 45 Alexion 11 Alnylam 14 0 Vertex 21 0 + Confidential and Proprietary 0 ^Approvals for rare disease indications * Expected based on current pipeline ultragenyx#5Keys to our success: Experienced team focused on innovation, speed, and execution Deep scientific understanding increases probability of success 82% demonstrate clinical success First ever regulatory and development approaches Approved products based on novel trial designs and endpoints Fastest development in the industry Global commercial organization Avg 5.5 yrs from clinic to approval Treating patients in ~34 countries 5 Confidential and Proprietary ultragenyx#6Revenue ($M) 2024 revenue growth expected to be ~20% driven by Crysvita in the U.S. and Latin America Annual Revenue Growth¹ 500 400 300 200 100 $28M 2018a $103M 2019a $182M 2020a $266M 2021a $356M 2022a 1 Excludes Bayer and Daiichi collaboration revenue and includes preliminary estimates for 2023 and 2024 Confidential and Proprietary $434M Product $500-530M 2023 Actual 2024 Guidance Crysvita¹ $328M $375-400M 14% to 22% growth Dojolvi $71M $75-80M 6% to 13% growth 2023a 2024e $500-530M Total Revenue² $434M 15% to 22% growth 1 Total Crysvita revenue, including North America, Latin America, and Europe 2 Total Revenue includes Crysvita, Dojolvi, Mepsevii, and Evkeeza ultragenyx#7Capital allocation focused on key clinical and commercials programs Uses of Cash1 11 Declining YoY Cash Used in Operations expected to be less than $400M in 2024 Ongoing revenue growth and continued expense management create path to profitability in 2026 Cash and equivalents² of $777M as of December 31, 2023 2022a 2023a 2024e ■Cash Used in Operations ■GTMF CapEx/Non-recurring 1 Cash used in operations, Gene Therapy Manufacturing Facility (GTMF) Capital Expenses and select non-recurring uses of cash; estimated values for 2024 2 Cash, cash equivalents, and available-for-sale investments as of December 31, 2023 7 Confidential and Proprietary ultragenyx#8COMMERCIAL DEVELOPMENT Focused on three therapeutic areas BONE ENDOCRINE Ph 3 Ph 2 INBORN ERRORS OF METABOLISM Ph 3 Ph 3 Ph 3 UX143 UX701 Osteogenesis Imperfecta Wilson DTX301 OTC DTX401 GSDla UX111 MPS IIIA CRYSVITAⓇ burosumab R CRYSVITAⓇ burosumab XLH Confidential and Proprietary TIO Mepsevii (vestronidase alfa-vjbk) injection DOJOLVI TRIHEPTANOIN Oral Liquid MPS VII LC-FAOD Evkeeza (evinacumab-dgnb) Injection HoFH CNS / MUSCLE Ph 2 GTX-102 Angelman Syndrome Preclinical (Disclosed) UX810 Duchenne UX055 CDD ultragenyx#9Diverse commercial and clinical pipeline. Candidate Kyowa Kirin CRYSVITA Mepsevii Description Pre-Clinical IND Phase 1 Anti-FGF23 Monoclonal Antibody X-Linked Hypophosphatemia (XLH) & Tumor-Induced Osteomalacia (TIO) Enzyme Replacement Mucopolysaccharidosis Type VII (MPS VII) Regeneron Anti-ANGPTL3 2 Homozygous Familial Hypercholesterolemia (HoFH) Evkeeza® Monoclonal Antibody² Mereo Biopharma Osteogenesis Imperfecta (OI) Anti-Sclerostin Monoclonal Antibody Substrate Replacement UX143 (setrusumab) DOJOLVI UX111 (ABO-102) AAV9 Gene Therapy DTX401 AAV8-G6Pase Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD) Sanfilippo Syndrome (MPS IIIA) Glycogen Storage Disease Type la (GSDIa) DTX301 Gene Therapy AAV8-OTC Gene Therapy Ornithine Transcarbamylase (OTC) Deficiency UX701 AAV9-ATP7B Gene Therapy Wilson Disease (WD) AAV9 UX055 CDKL5 Deficiency Disorder Gene Therapy Microdystrophin UX810 Duchenne Muscular Dystrophy Gene Therapy GTX-102 Antisense Oligonucleotide Angelman Syndrome (AS) 1: Prevalence in commercially accessible geographies 2: Ultragenyx licensed ex-US rights to Evkeeza from Regeneron 3: Excludes the US, where Regeneron has rights 9 Confidential and Proprietary Phase 2 Phase 3 Approved Prevalence¹ Key Protein Biologic Small Molecule Gene Therapy Nucleic Acid ~50,000 ~200 ~3,000 5,000³ ~60,000 ~8,000 14,000 ~3,000 - 5,000 ~6,000 ~10,000 ~50,000 ~20,000 30,000 ~40,000 ~60,000 ultragenyx#10Three opportunities for significant near-term value creation. 10 Osteogenesis Imperfecta Confidential and Proprietary Angelman Syndrome Wilson Disease ultragenyx#11UX143 (setrusumab) for osteogenesis imperfecta: Phase 2 data showed 67% reduction in AFR post-treatment Radiographically Confirmed Fractures¹ 2 Phase 3 Endpoint (excluding Fingers, Toes, Face, and Skull) P=0.042 SUPER MAHO Median Annualized Fracture Rate (AFR) 0.5 1.5 1 0.72 0.0 0 Pre- Treatment² After Setrusumab Initiation 1: Data presented at the company's Analyst Day on October 16, 2023 2: Pre-Treatment period includes fractures in the two years before screening based on medical record review and patient report, and fractures between screening and first dose 11 Confidential and Proprietary Data presented at the company's Analyst Day on October 16, 2023 6 y/o male patient with Type IV OI, increased mobility after 17 months on study ultragenyx#12GTX-102 for Angelman syndrome: Phase 1/2 showed meaningful and improving changes across multiple domains at longer timepoints¹ IIII & Quantitative improvements in Bayley-4 far exceeding natural history • • Cognition Receptive Communication Gross Motor Improvements in ASA show meaningful reductions in severity • Sleep • Behavior Supportive data from . EEG delta power and sleep spindle Enrollment in Phase 1/2 complete with 74 patients enrolled across Cohorts 1 to 7 and A through E 1: Data presented at the company's Analyst Day on October 16, 2023 12 Confidential and Proprietary ultragenyx#13GTX-102: Multi-Domain Responder Index (MDRI) captures broad clinical benefit across five domains and multiple endpoints 13 Patient ASA ASA (n=11) Sleep Behavior Bayley-4 Receptive Comm Total Bayley-4 Bayley-4 Gross Motor Cognition Net Responses* Minimal Important Difference (MID) 1 1 0 1 0 3 1 . ASA-Sleep +/- 1 2 3 2 7 3 17 4 ASA-Behavior +/- 1 3 1 1 16 5 20 (л 5 4 0 0 14 3 23 2 Bayley-4 Receptive Communication +/-6 5 1 2 6 1 4 3 • Bayley-4 Gross Motor +/- 5 6 4 0 7 1 1 2 • Bayley-4 Cognition +/- 5 7 2 1 10 9 16 5 8 00 1 1 15 6 25 5 9 2 0 23 7 11 2 Median Total Net Responses 10 n/a n/a 2 1 5 1 Net Responses #0 11 0 0 3 4 16 1 Decline *Day 338 +2 p** = 0.001 ** P-value is from a sign test Improvement Data presented at the company's Analyst Day on October 16, 2023 Confidential and Proprietary ultragenyx#14UX701 for Wilson Disease: Four of five in Cohort 1 tapering SOC, including two completely off chelators and/or zinc therapy 1 Cohort 1 Weeks on Study Reduction of SOC [Chelator and/or zinc therapy] Copper Trafficking Patient 1 82 0% Patient 2 70 100% Patient 3 44 100% Patient 4 20 33% Patient 5 16 50% 1: Data presented at the company's Analyst Day on October 16, 2023 14 Confidential and Proprietary Indeterminate Reduced urinary copper and improved trafficking by copper oxidase assay Reduced urinary copper and improved trafficking by copper oxidase assay Reduced urinary copper; pending trafficking assessment Reduced urinary copper; pending trafficking assessment ultragenyx#15Four pivotal gene therapy programs DTX401 for GSDla • HEK293 manufacturing process . Phase 3 fully enrolled • Data anticipated in 1H24 . DTX301 for OTC HEK293 manufacturing process ⚫ Phase 3 FPI in February 2023 Expect Ph3 to be fully enrolled in 1H24 15 Confidential and Proprietary M UX111 for MPS IIIA • HEK293 manufacturing process • Updated pivotal data presented at WORLDSymposium TM in February 2024 Seeking accelerated review path with FDA UX701 for Wilson disease • Pinnacle PCLTM manufacturing process Phase 1/2/3 study ongoing Stage 1 enrollment completed in January 2024 & data expected mid-2024 ultragenyx#16Gene therapy platform built on best-in-class manufacturing capabilities Manufacturing facility in Bedford, MA Pinnacle PCL™ platform Efficient, reliable production of AAV Improved product quality and yield Lower cost and increased speed of production Potentially improved safety of AAV therapy at higher doses Facility capable of running both HEK and Pinnacle PCL 16 Confidential and Proprietary ultragenyx#17Near-term key clinical catalysts PROGRAM UX143 Osteogenesis Imperfecta GTX-102 Angelman Syndrome UX701 Wilson Disease DTX401 GSDla OBJECTIVE Complete enrollment of Phase 3 Orbit study Complete enrollment of Phase 3 Cosmic Further Phase 2 data update LPI for Expansion Cohorts Phase 1/2 Expansion data End of Phase 2 Discussion with FDA Stage 1 enrollment completion Stage 1 safety and initial efficacy data Initiation of Stage 2 Phase 3 data Timing 1Q 2024 1H 2024 2H 2024 ✓ 1H 2024 Mid-2024 ✓ Mid-2024 2H 2024 1H 2024 DTX301 Phase 3 enrollment completion 1H 2024 OTC deficiency ultragenyx 17 Confidential and Proprietary#18We are leading the future of rare disease medicine Most productive rare disease company in the industry Near-term catalysts for key clinical programs QQQ 窗窗窗 Expect multiple blockbuster product approvals in 2-3 years $ Revenue growth and expense management support path to profitability 18 Confidential and Proprietary ultragenyx#19ultragenyx Appendix Confidential and Proprietary#20Key licenses & intellectual property – Commercial products Product CRYSVITAⓇ (XLH, TIO) MEPSEVII® (MPS 7) License Kyowa Kirin Co. (KKC) St. Louis University (Know-How) N/A (IP Owned by Ultragenyx) Baylor Research Institute (BRI) DOJOLVIⓇ (LC-FAOD) N/A (IP Owned by Ultragenyx) Product License EVKEEZA® (HOFH) Regeneron Includes granted U.S. patent term extension 2Includes projected U.S. patent term extension ³Includes projected extension via supplementary protection certificates (SPCs) 20 Confidential and Proprietary US Intellectual Property Rights/Royalties • Anti-FGF23 antibodies and use for treatment of XLH and TIO (2023-2032)¹ Q2W dosing for treatment of FGF23-associated hypophosphatemic disorders (2035) See discussion of KKC license and collaboration in annual report for royalty summary Low single-digit royalty until expiration of orphan drug exclusivity Recombinant human GUS (rhGUS) and use for treatment of MPS7 (2035) Compositions comprising triheptanoin (2025-2029)² Mid single-digit royalty Ultrapure triheptanoin and use in treatment of FAOD (Pending; 2034) EU Intellectual Property Rights/Royalties + Milestones Evkeeza antibody and use for treatment of HOFH (2036)³ Evkeeza antibody in combination with other agents for treatment of HOFH (Pending: 2037) Stabilized formulations of Evkeeza (Pending: 2041) Regeneron supplies product and charges Ultragenyx a transfer price from the low 20% range up to 40% on net sales Ultragenyx to pay up to $63M in potential regulatory and sales milestones ultragenyx#21Key licenses & intellectual property - Clinical programs. Product License UX143 Mereo Biopharma (Osteogenesis Imperfecta) DTX401 (GSDIa) US Intellectual Property Rights/Royalties + Milestones Setrusumab antibody (2028) ° Use of anti-sclerostin antibodies including setrusumab for treatment of OI (2037) ° • Tiered double-digit royalty on ex-EU sales and clinical, regulatory, and commercial milestones to Mereo Fixed double-digit royalty on EU sales to Ultragenyx ° Sub-License from REGENXBIO of UPENN IP AAV8 Capsid (2024) • NIH (Non-Exclusive) • Low to mid single-digit royalty and development milestones Recombinant vectors comprising codon-optimized G6Pase gene (2034) Low single-digit royalty Recombinant vectors comprising SGSH gene (Pending; 2032) UX111/ABO-102 Nationwide Children's Hospital (NCH) • (MPS IIIA) Development milestones up to $1M plus low single-digit royalty Abeona Therapeutics DTX301 Sub-License from REGENXBIO of UPENN IP ° (OTC Deficiency) Sub-License from REGENXBIO of UPENN IP • UX701 (Wilson Disease) UPENN N/A (IP Owned by Ultragenyx) Texas A&M University GTX-102 (Angelman Syndrome) GeneTx 21 Confidential and Proprietary • • Commercial milestones up to $30M plus tiered royalty up to 10% AAV8 Capsid (2024) Recombinant vectors comprising codon-optimized OTC gene (2035) Low to mid single-digit royalty and development milestones AAV9 Capsid (2024-2026) Mid to high single-digit royalty and up to $9M in development milestones Recombinant vectors comprising certain regulatory and coding sequences packaged in UX701 (2039) Development up to $5M and commercial milestones up to $25M plus low to mid single-digit royalty Recombinant vectors expressing a novel truncated version of ATP7B protein produced by UX701 (Pending; 2040) Use of UBE3A-ATS antisense oligonucleotides including GTX-102 for treatment of AS (2038) Development and commercial milestones plus mid single-digit royalty Development, regulatory, and commercial milestones up to $190M plus mid to high single-digit royalty ultragenyx#22CRYSVITA® Exclusivity summary United States XLH Orphan Exclusivity TIO Orphan Exclusivity Biologics Exclusivity Crysvita COM Patent Q2W Dosing Patent 2025 2027 2030 2032* 2035 CRYSVITA burosumab 2018 2020 2022 2024 2026 2028 2030 2032 2034 2036 Europe *Includes projected US PTE and EU SPC awards 22 Confidential and Proprietary 2028 XLH Orphan D&M Exclusivity -- 2033* Crysvita COM Patent 2035 Q2W Dosing Patent ultragenyx#23DOJOLVIⓇ Exclusivity summary United States DOJOLVI TRIHEPTANOIN Oral Liquid NCE Exclusivity LC-FAOD Orphan Exclusivity Dojolvi COM Patent Ultrapure Dojolvi (Pending) 2025 2027 2029* 2034 2018 2020 2022 2024 2026 2028 2030 2032 2034 2036 Europe *Includes projected US PTE award 23 Confidential and Proprietary 2034 Ultrapure Dojolvi (Pending) ultragenyx#24MEPSEVII® Exclusivity summary 24 United States MPS7 Orphan Exclusivity Biologics Exclusivity 2024 2029 Mepsevii (vestronidase alfa-vjbk) injection, for intravenous use 10 mg/5 mL (2 mg/mL) Mepsevii COM Patent 2035 2018 2020 2022 2024 2026 2028 2030 2032 2034 2036 Europe Confidential and Proprietary 2028 MPS7 Orphan + D&M Exclusivity 2035 Mepsevii COM Patent ultragenyx#25EVKEEZA® Exclusivity summary Europe Data & Marketing Exclusivity 2031 Evkeeza Ab Patent 2036* EvkeezaⓇ (evinacumab-dgnb) Injection 2022 2024 2026 2028 2030 2032 2034 2036 2038 2040 *Includes projected EU SPC award 25 Confidential and Proprietary Exemplary additional patent applications pending: • Evkeeza w/ PCSK9 Ab • Evkeeza w/ statins . Evkeeza formulations Projected expiration dates between 2037-2041 ultragenyx