Exhibit 99.1 Protagonist Reports First Quarter 2024 Financial Results and Provides Corporate Update Entered into a worldwide license and collaboration agreement for rusfertide with Takeda; Cash runway extended through Q4 2027 Enrollment in both Phase 3 ICONIC LEAD and ICONIC TOTAL trials of JNJ-2113 in patients with moderate to severe psoriasis is now complete Data from the Phase 2b FRONTIER 2, a 52-week long term extension study of JNJ-2113 presented at the American Academy of Dermatology 2024 Annual Meeti ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 98-0505495 (State or other j ...

Exhibit 99.1 Protagonist Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Corporate Update Worldwide collaboration agreement executed with Takeda Pharmaceuticals, including a $300 million upfront payment for rusfertide in polycythemia vera and other hematological indications Cash runway extended through Q4 2027 Two articles published in the New England Journal of Medicine reporting results from the Phase 2b FRONTIER 1 study of JNJ-2113 and the Phase 2 REVIVE study of rusfertide Our P ...

PART I [Condensed Consolidated Financial Statements (unaudited)](index=4&type=section&id=Item%201.%20Condensed%20Consolidated%20Financial%20Statements%20%28unaudited%29) Unaudited condensed financial statements report a $106.3 million net loss for the first nine months of 2023, with cash and equivalents increasing to $322.7 million, boosted by financing and a $50.0 million post-period milestone Condensed Consolidated Balance Sheet Data (in thousands) | | September 30, 2023 | December 31, 2022 | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $230,527 | $125,744 | | Marketable securities | $92,209 | $111,611 | | Total current assets | $324,881 | $243,077 | | Total assets | $330,016 | $247,928 | | **Liabilities and Stockholders' Equity** | | | | Total current liabilities | $27,867 | $31,179 | | Total liabilities | $27,867 | $32,320 | | Total stockholders' equity | $302,149 | $215,608 | Condensed Consolidated Statements of Operations (in thousands, except per share data) | | Three Months Ended Sep 30, | Nine Months Ended Sep 30, | | :--- | :--- | :--- | | | **2023** | **2022** | **2023** | **2022** | | License and collaboration revenue | $0 | $0 | $0 | $26,581 | | Research and development | $30,664 | $25,402 | $91,262 | $96,331 | | General and administrative | $7,662 | $6,901 | $25,439 | $25,107 | | Loss from operations | $(38,326) | $(32,303) | $(116,701) | $(94,857) | | Net loss | $(34,105) | $(31,232) | $(106,290) | $(93,199) | | Net loss per share, basic and diluted | $(0.58) | $(0.64) | $(1.91) | $(1.90) | Condensed Consolidated Statements of Cash Flows (in thousands) | | Nine Months Ended September 30, | | :--- | :--- | :--- | | | **2023** | **2022** | | Net cash used in operating activities | $(87,196) | $(76,502) | | Net cash provided by investing activities | $22,029 | $87,533 | | Net cash provided by financing activities | $169,950 | $18,285 | - On November 1, 2023, the company announced it had earned a **$50.0 million** milestone payment from its collaboration with Janssen, triggered by the dosing of the third patient in the ICONIC-TOTAL Phase 3 clinical trial of JNJ-2113[74](index=74&type=chunk) [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=28&type=section&id=Item%202.%20Management%27s%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses financial performance and operational progress, highlighting rusfertide's Phase 3 advancement and JNJ-2113's entry into Phase 3, alongside increased net loss and strengthened balance sheet via financing - The company's lead clinical asset, rusfertide, is in a global **Phase 3** trial (VERIFY) for polycythemia vera (PV), with enrollment expected to be completed in the **first quarter of 2024**[79](index=79&type=chunk)[83](index=83&type=chunk) - The collaboration with Janssen on JNJ-2113 is advancing, with Janssen initiating three studies in October 2023: two **Phase 3** trials in psoriasis (ICONIC-LEAD, ICONIC-TOTAL) and one **Phase 2b** trial in ulcerative colitis (ANTHEM-UC)[90](index=90&type=chunk)[92](index=92&type=chunk) Comparison of Results of Operations (in thousands) | | Nine Months Ended Sep 30, 2023 | Nine Months Ended Sep 30, 2022 | Change ($) | Change (%) | | :--- | :--- | :--- | :--- | :--- | | License and collaboration revenue | $0 | $26,581 | $(26,581) | (100)% | | Research and development | $91,262 | $96,331 | $(5,069) | (5)% | | General and administrative | $25,439 | $25,107 | $332 | 1% | | Loss from operations | $(116,701) | $(94,857) | $(21,844) | 23% | | Net loss | $(106,290) | $(93,199) | $(13,091) | 14% | - The company raised significant capital in 2023, including approximately **$107.8 million** from a public offering, **$24.3 million** from an ATM facility, and **$34.4 million** from warrant exercises[128](index=128&type=chunk)[129](index=129&type=chunk)[133](index=133&type=chunk) - As of September 30, 2023, the company had **$322.7 million** in cash, cash equivalents, and marketable securities, which management believes is sufficient to fund operations for at least the next **12 months**[135](index=135&type=chunk)[182](index=182&type=chunk) [Quantitative and Qualitative Disclosures About Market Risk](index=51&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) This section details the company's market risk exposure, primarily from interest rate fluctuations and inflation, concluding that neither has had a significant material effect on financial results - The company's exposure to interest rate risk is considered not significant, with a hypothetical **100 basis point** change in interest rates not expected to have a significant impact on its portfolio's value[149](index=149&type=chunk) - The company does not believe that inflation has had a material effect on its results of operations during the three and nine months ended September 30, 2023[151](index=151&type=chunk) - Foreign currency risk is considered minimal, as a **10%** change in exchange rates would not materially affect the results of operations. Cash held in Australia was approximately **$1.2 million** as of September 30, 2023[150](index=150&type=chunk) [Controls and Procedures](index=53&type=section&id=Item%204.%20Controls%20and%20Procedures) Management, including the CEO and CFO, concluded that disclosure controls and procedures were effective as of September 30, 2023, with no material changes to internal control over financial reporting - The CEO and CFO concluded that the company's disclosure controls and procedures were effective as of September 30, 2023[152](index=152&type=chunk) - There were no changes in the company's internal control over financial reporting during the most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, internal controls[154](index=154&type=chunk) PART II [Legal Proceedings](index=54&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently involved in any material legal proceedings and is unaware of any pending or threatened litigation - The company is not currently a party to any material legal proceedings[155](index=155&type=chunk) [Risk Factors](index=54&type=section&id=Item%201A.%20Risk%20Factors) This section outlines key risks including dependence on clinical success, high development costs, a history of losses, need for capital, reliance on third parties, regulatory hurdles, and macroeconomic instability - The company is **heavily dependent** on the success of its clinical product candidates, and failure in clinical development, which is a **lengthy and expensive process** with an uncertain outcome, would substantially harm the business[158](index=158&type=chunk)[163](index=163&type=chunk)[165](index=165&type=chunk) - The company has a history of significant losses (**$643.0 million** accumulated deficit as of Sep 30, 2023) and expects to incur losses for the foreseeable future, requiring substantial additional funding[158](index=158&type=chunk)[179](index=179&type=chunk)[181](index=181&type=chunk) - The business **relies on** its collaboration with Janssen for the development and commercialization of JNJ-2113 and on third-party CROs and manufacturers for its clinical trials and drug supply[158](index=158&type=chunk)[186](index=186&type=chunk)[191](index=191&type=chunk) - **Significant risks** exist related to obtaining regulatory approval, including potential for trial delays or failure, and even if approved, products may not achieve market acceptance or favorable reimbursement[160](index=160&type=chunk)[197](index=197&type=chunk)[210](index=210&type=chunk) - The company's success **depends on** its ability to obtain and protect intellectual property rights for its product candidates and technologies, which is uncertain and can be challenged[160](index=160&type=chunk)[246](index=246&type=chunk) - **Unstable market and economic conditions**, including inflation and financial institution instability, pose risks to the company's business, financial condition, and access to capital[160](index=160&type=chunk)[220](index=220&type=chunk)[223](index=223&type=chunk) [Unregistered Sales of Equity Securities and Use of Proceeds](index=100&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) The company reported no unregistered sales or repurchases of equity securities during the period - There were no unregistered sales of equity securities during the period[286](index=286&type=chunk) [Defaults Upon Senior Securities](index=100&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) The company reported no defaults upon its senior securities - None[288](index=288&type=chunk) [Mine Safety Disclosures](index=100&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This item is not applicable to the company's business - Not applicable[289](index=289&type=chunk) [Other Information](index=100&type=section&id=Item%205.%20Other%20Information) The company did not report any other information for this item - None[290](index=290&type=chunk) [Exhibits](index=100&type=section&id=Item%206.%20Exhibits) This section provides an index of exhibits filed with the quarterly report, including certifications and XBRL data files - The report includes an index of all exhibits filed, such as certifications required under Sections 302 and 906 of the Sarbanes-Oxley Act[292](index=292&type=chunk)

Table of Contents ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q Delaware 98-0505495 (State or oth ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 98-0505495 (State or other j ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 98-0505495 (State o ...

1 COMPANY OVERVIEW Dinesh V. Patel, PhD | President & CEO August 4, 2022 This presentation and the accompanying oral presentation contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, business strategy, product candidates, capital resources, potential m ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 98-0505495 (State or oth ...