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Item 1. Financial Statements

2025-11-10 compared with 2025-08-07 · 256 added, 218 removed, 795 unchanged (37% of the section changed)

2 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED BALANCE SHEETS

(dollars in thousands, except per share amounts) June 30,

(dollars in thousands, except per share amounts) September 30,

2025 December 31,

28 unchanged sentences

Preferred stock $ 0.00001 par value;

25,000,000 shares authorized at June 30, 2025 and December 31, 2024;

no shares issued and outstanding at June 30, 2025 and December 31, 2024

25,000,000 shares authorized at September 30, 2025 and December 31, 2024;

no shares issued and outstanding at September 30, 2025 and December 31, 2024

Common stock $ 0.00001 par value;

350,000,000 shares authorized at June 30, 2025 and December 31, 2024;

263,041,832 and 224,848,992 shares issued and outstanding at June 30, 2025 and December 31, 2024, respectively

350,000,000 shares authorized at September 30, 2025 and December 31, 2024;

265,226,038 and 224,848,992 shares issued and outstanding at September 30, 2025 and December 31, 2024, respectively

Additional paid-in capital 1,713,045 1,629,167

8 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS)

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(dollars in thousands, except per share amounts) 2025 2024 2025 2024

18 unchanged sentences

Loss on extinguishment of debt — — — ( 517 )

Net income (loss) before income taxes $ 247 $ ( 8,582 ) $ 6,359 $ ( 26,567 )

Income (loss) before income taxes 1,155 ( 20,039 ) 7,514 ( 46,606 )

Income tax expense ( 615 ) — ( 615 ) —

Net income (loss) $ 540 $ ( 20,039 ) $ 6,899 $ ( 46,606 )

11 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (DEFICIT)

Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Income

Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Income Accumulated

Deficit Total Stockholders'

13 unchanged sentences

Restricted stock unit vesting 451,104 — — — — —

— — — — ( 8,582 ) ( 8,582 )

Net loss — — — — ( 8,582 ) ( 8,582 )

Balance at June 30, 2024 209,929,145 $ 2 $ 1,601,755 $ 6 $ ( 1,635,517 ) $ ( 33,754 )

Issuance of common stock, net of

issuance costs 1,242,662 — 1,662 — — 1,662

Proceeds from sale of stock under

employee stock purchase plan 97,411 — 83 — — 83

Exercise of options 2,312 — — — — —

Stock-based compensation expense — — 1,646 — — 1,646

Restricted stock unit vesting 270,592 — — — — —

Net loss — — — — ( 20,039 ) ( 20,039 )

Balance at September 30, 2024 211,542,122 $ 2 $ 1,605,146 $ 6 $ ( 1,655,556 ) $ ( 50,402 )

Common Stock Additional Paid-In

Capital Accumulated Other Comprehensive Income

Capital Accumulated Other Comprehensive Income Accumulated

Deficit Total Stockholders'

16 unchanged sentences

Restricted stock unit vesting 451,246 — — — — —

— — — — 247 247

Net income — — — — 247 247

Balance at June 30, 2025 263,041,832 $ 2 $ 1,701,217 $ 6 $ ( 1,672,001 ) $ 29,224

Warrants exercised, cashless

1,408,588 — 7,494 — — 7,494

Proceeds from sale of stock under

employee stock purchase plan 94,060 — 151 — — 151

Exercise of options 438,300 — 962 — — 962

Stock-based compensation expense — — 3,221 — — 3,221

Restricted stock unit vesting 243,258 — — — — —

— — — — 540 540

Balance at September 30, 2025 265,226,038 $ 2 $ 1,713,045 $ 6 $ ( 1,671,461 ) $ 41,592

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

3 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Six Months Ended June 30,

Nine Months Ended September 30,

(dollars in thousands) 2025 2024

28 unchanged sentences

Proceeds from the sale of property and equipment 172 —

Net cash provided by (used in) investing activities 28 ( 29 )

Net cash used in investing activities ( 49 ) ( 31 )

Financing Activities:

11 unchanged sentences

Issuance of warrants in connection with BlackRock Credit Agreement $ 2,199 $ 4,846

Unpaid issuance costs related to BlackRock Credit Agreement $ — $ 522

Cashless exercise of warrants in connection with BlackRock Credit Agreement $ 7,494 $ —

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

21 unchanged sentences

In addition, the Company continues to explore additional development opportunities to expand its pipeline and portfolio of novel therapeutics.

As of June 30, 2025, the Company had cash and cash equivalents of approximately $ 137.3 million.

As of September 30, 2025, the Company had cash and cash equivalents of approximately $ 166.4 million.

Based on its current operating plan, the Company believes that its cash resources and the cash the Company expects to generate from product, royalty, supply and license revenues will be sufficient to fund its current operating plan for at least twelve months from the filing of this Quarterly Report on Form 10-Q, or Form 10-Q .

However, if the Company’s operating performance deteriorates significantly from the levels expected in the Company’s operating plan, it would affect the Company’s liquidity and its ability to continue as a going concern in the future.

However, if the Company’s operating performance deteriorates significantly from the levels expected in the Company’s operating plan, including if the Company does not achieve its future anticipated Vafseo revenue projections, it would affect the Company’s liquidity and its ability to continue as a going concern in the future.

The Company expects to finance future cash needs through product and license, collaboration and other revenue, including royalties and revenue from supply agreements.

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In the opinion of management, all adjustments, consisting of normal recurring accruals and revisions of estimates, considered necessary for a fair presentation of the unaudited condensed consolidated financial statements have been included.

Interim results for the three and six months ended June 30, 2025 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2025 or any other future period.

Interim results for the three and nine months ended September 30, 2025 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2025 or any other future period.

Basis of Presentation and Principles of Consolidation

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In determining its cash, cash equivalents and restricted cash, the Company considers only those highly liquid investments, readily convertible to cash within 90 days from the date of purchase to be cash equivalents.

As of June 30, 2025, cash and cash equivalents primarily included cash on hand and money market funds.

As of September 30, 2025, cash and cash equivalents primarily included cash on hand and money market funds.

Restricted cash represents amounts required to secure the outstanding letter of credit in connection with the Company’s office and laboratory space in Cambridge, Massachusetts, or the Cambridge Lease .

Restricted cash is included in “other long-term assets” in the consolidated balance sheets.

Restricted cash is included in "prepaid expenses and other current assets" in the consolidated balance sheet as of September 30, 2025 and in “other long-term assets” in the consolidated balance sheet as of December 31, 2024.

The following table reconciles cash, cash equivalents and restricted cash reported within the Company's consolidated balance sheets to the total amounts shown in the consolidated statements of cash flows:

(in thousands) June 30, 2025 December 31, 2024

(in thousands) September 30, 2025 December 31, 2024

Cash and cash equivalents $ 166,444 $ 51,870

Restricted cash included in other long-term assets 1,690 1,680

Restricted cash 1,695 1,680

Total cash, cash equivalents and restricted cash $ 168,139 $ 53,550

7 unchanged sentences

The Company believes that credit risks associated with its customers and collaboration partners are not significant.

The Company's allowance for credit losses was $ 2.2 million and $ 1.2 million as of June 30, 2025 and December 31, 2024, respectively.

The Company's allowance for credit losses was $ 2.6 million and $ 1.2 million as of September 30, 2025 and December 31, 2024, respectively.

The following table summarizes the activity related to the Company's allowance for credit losses (in thousands):

3 unchanged sentences

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Six Months Ended June 30,

Nine Months Ended September 30,

Beginning balance $ 1,212 $ 1,029

12 unchanged sentences

The Company is currently evaluating ASU 2023-09 and does not expect it to have a material effect on the Company’s consolidated financial statements.

In November 2024, the FASB issued an accounting standards update, ASU 2024-03, which requires new tabular disclosures in the notes to consolidated financial statements, disaggregating certain cost and expense categories within relevant captions on the consolidated statements of operations and comprehensive income (loss).

In November 2024, the FASB issued ASU 2024-03, Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40):

Disaggregation of Income Statement Expenses , which requires new tabular disclosures in the notes to consolidated financial statements, disaggregating certain cost and expense categories within relevant captions on the consolidated statements of operations and comprehensive income (loss).

The prescribed cost and expense categories requiring disaggregated disclosures include purchases of inventory, employee compensation, depreciation and intangible asset amortization, along with certain other expense disclosures already required by GAAP that would need to be integrated within the new tabular disaggregated expense disclosures.

4 unchanged sentences

The Company is currently reviewing the impact that the adoption of ASU 2024-03 may have on its expense disclosures in the notes to the consolidated financial statements.

In July 2025, the FASB issued ASU 2025-05, Financial Instruments - Credit Losses (Topic 326):

Measurement of Credit Losses for Accounts Receivable and Contract Assets .

ASU 2025-05 provides a practical expedient that all entities can use when estimating expected credit losses for current accounts receivable and current contract assets arising from transactions accounted for under ASC 606, Revenue from Contracts with Customers .

Under this practical expedient, an entity is allowed to assume that the current conditions it has applied in determining credit loss allowances for current accounts receivable and current contract assets remain unchanged for the remaining life of those assets.

ASU 2025-05 is effective for fiscal years beginning after December 15, 2025, and interim reporting periods in those years.

Entities that elect the practical expedient and, if applicable, make the accounting policy election are required to apply the amendments prospectively.

The Company is currently evaluating ASU 2025-05 and does not expect it to have a material effect on the Company’s consolidated financial statements.

In September 2025, the FASB issued ASU 2025-06, Intangibles - Goodwill and Other - Internal-Use Software , which removes all references to prescriptive and sequential software development stages (referred to as "project stages").

An entity will be required to start capitalizing software costs when (i) management has authorized and committed to funding the software project and (ii) it is probable that the project will be completed and the software will be used to perform the function intended (referred to as the "probable-to-complete recognition threshold").

ASU 2025-06 is effective for fiscal years beginning after December 15, 2027, and interim reporting periods within those annual periods.

Early adoption is permitted as of the beginning of the annual reporting period.

The Company is currently evaluating ASU 2025-06 and does not expect it to have a material effect on the Company’s consolidated financial statements.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 8

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

FAIR VALUE OF FINANCIAL INSTRUMENTS

The tables below present certain assets and liabilities measured at fair value categorized by the level of input used in the valuation of each asset and liability (in thousands):

June 30, 2025

September 30, 2025

Level 1 Level 2 Level 3 Total Fair Value

7 unchanged sentences

Warrant liability $ — $ 5,176 $ — $ 5,176

Akebia Therapeutics, Inc.

| Form 10-Q | Page 8

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Cash and cash equivalents — Money market funds included within cash and cash equivalents are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets.

3 unchanged sentences

Inventories consists of the following (in thousands):

June 30, 2025 December 31, 2024

September 30, 2025 December 31, 2024

Inventories, current:

7 unchanged sentences

Total inventories $ 58,503 $ 51,196

Inventory written down as a result of excess, obsolescence, scrap or other reasons charged to cost of product and other revenue in the unaudited condensed consolidated statements of operations and comprehensive income (loss) was immaterial and $ 0.1 million during the three and six months ended June 30, 2025, respectively, and $ 0.5 million and $ 1.1 million during the three and six months ended June 30, 2024, respectively.

For the three and six months ended June 30, 2024, the Company realized lower cost of product and other revenue of $ 4.9 million and $ 8.6 million, respectively, due to the Company's ability to sell inventory previously written down to zero, its then net realizable value.

Inventory written down as a result of excess, obsolescence, scrap or other reasons charged to cost of product and other revenue in the unaudited condensed consolidated statements of operations and comprehensive income (loss) was $ 0.5 million and $ 0.6 million during the three and nine months ended September 30, 2025, respectively, and $ 1.3 million and $ 2.4 million during the three and nine months ended September 30, 2024, respectively.

For the three and nine months ended September 30, 2024, the Company realized lower cost of product and other revenue of $ 3.7 million and $ 12.3 million, respectively, due to the Company's ability to sell inventory previously written down to zero, its then net realizable value.

INTANGIBLE ASSET AND GOODWILL

4 unchanged sentences

The intangible asset was fully amortized as of December 31, 2024.

The Company recorded $ 9.0 million and $ 18.0 million in amortization expense for the three and six months ended June 30, 2024, respectively, related to the developed product rights for Auryxia.

As of each of June 30, 2025 and December 31, 2024, the Company had goodwill of $ 59.0 million in connection with the December 2018 merger with Keryx.

The Company recorded $ 9.0 million and $ 27.0 million in amortization expense for the three and nine months ended September 30, 2024, respectively, related to the developed product rights for Auryxia.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 9

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

As of each of September 30, 2025 and December 31, 2024, the Company had goodwill of $ 59.0 million in connection with the December 2018 merger with Keryx.

The Company has not identified any goodwill impairment to date.

1 unchanged sentence

Prepaid expenses and other current assets are as follows (in thousands):

Description June 30, 2025 December 31, 2024

Description September 30, 2025 December 31, 2024

Prepaid manufacturing $ — $ 4,029

Restricted cash

Other 5,331 7,321

3 unchanged sentences

Other prepaid expenses and other current assets, among other things, include capitalized implementation costs, prepaid insurance, prepaid clinical trial costs and prepaid information technology costs.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 9

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Other long-term assets are as follows (in thousands):

Description June 30, 2025 December 31, 2024

Description September 30, 2025 December 31, 2024

Long-term inventories $ 39,860 $ 34,953

4 unchanged sentences

Accrued expenses and other current liabilities consists of the following (in thousands):

June 30, 2025 December 31, 2024

September 30, 2025 December 31, 2024

Product revenue allowances excluding rebates $ 8,972 $ 9,657

15 unchanged sentences

Entry into BlackRock Loan Facility

On January 29, 2024, or the Closing Date , the Company entered into the Agreement for the Provision of a Loan Facility, or the BlackRock Credit Agreement, with Kreos Capital VII (UK) Limited , or Kreos , which are funds and accounts managed by BlackRock Inc., collectively, BlackRock , and provides for a senior secured term loan facility in the aggregate principal amount of up to $ 55.0 million, or the Term Loan Facility .

Akebia Therapeutics, Inc.

| Form 10-Q | Page 10

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

of up to $ 55.0 million, or the Term Loan Facility .

The Term Loan Facility was available in three tranches (i) Tranche A — $ 37.0 million was funded on the Closing Date and used to repay the Pharmakon Term Loans (as defined below);

2 unchanged sentences

Tranche C was available subject to receipt of a certain amount of cumulative gross cash proceeds after the Closing Date in the form of equity or equity linked securities in one or more series of transactions.

The terms of the Extended Tranche C are substantially similar to the terms of the original Tranche C, however, interest will accrue on the Extended Tranche C as if it was advanced on December 31, 2024.

The terms of the Extended Tranche C are substantially similar to the terms of the original Tranche C, however, interest accrued on the Extended Tranche C as if it was advanced on December 31, 2024.

On the Closing Date, the Company received $ 34.5 million on Tranche A, after deducting debt issuance costs, fees and expenses.

2 unchanged sentences

The BlackRock Term Loan Facility had an initial maturity date of March 31, 2025, which was automatically extended to January 29, 2028, after the Company received FDA approval for Vafseo, or the BlackRock Maturity Date .

The Company is required to make interest-only payments until December 31, 2026, or the BlackRock Interest Only Period , after which the Company will

Akebia Therapeutics, Inc.

| Form 10-Q | Page 10

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

begin paying equal monthly principal on the first calendar day of each month.

The Company is required to make interest-only payments until December 31, 2026, or the BlackRock Interest Only Period , after which the Company will begin paying equal monthly principal on the first calendar day of each month.

In the event of certain prespecified events, the repayment schedule will be accelerated.

The Term Loan Facility will accrue interest at a floating annual rate equal to the sum of (i) the term Secured Overnight Financing Rate , or SOFR , for a tenor of one month (subject to a floor of 4.25 % per annum) plus (ii) a margin of 6.75 % per annum (subject to an overall cap of 15.00 % per annum on the all-in interest rate).

As of June 30, 2025, the Company's interest rate was 11.08 %.

The Company recognized interest expense related to the BlackRock Credit Agreement of $ 2.1 million and $ 4.1 million during the three and six months ended June 30, 2025, respectively, and $ 1.6 million and $ 3.8 million during the three and six months ended June 30, 2024, respectively.

As of September 30, 2025, the Company's interest rate was 11.00 %.

The Company recognized interest expense related to the BlackRock Credit Agreement of $ 2.1 million and $ 6.2 million during the three and nine months ended September 30, 2025, respectively, and $ 1.7 million and $ 5.5 million during the three and nine months ended September 30, 2024, respectively.

During the continuance of any payment event of default under the BlackRock Credit Agreement, the interest rate on such overdue sum will automatically increase by an additional 3.0 % per annum, and may be subject to an additional late fee of 2.0 % of such overdue sum.

2 unchanged sentences

If prepayment is made during the first year, the Company also is required to pay the amount of otherwise due interest payments for the twelve-month period following prepayment.

As of June 30, 2025, future principal payments under the BlackRock Credit Agreement are as follows (in thousands):

As of September 30, 2025, future principal payments under the BlackRock Credit Agreement are as follows (in thousands):

Principal Payments

6 unchanged sentences

If an event of default occurs and is continuing under the BlackRock Credit Agreement, BlackRock is entitled to take enforcement action, including acceleration of amounts due and it could limit the Company's ability to make certain payments under the Vifor Termination Agreement (as defined below).

On July 10, 2024, in connection with the Termination and Settlement Agreement entered into between the Company and CSL Vifor (as defined below), or the Vifor Termination Agreement , the Company and Kreos entered into a First Amendment to the BlackRock Credit Agreement, which amended certain provisions of the BlackRock Credit Agreement.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 11

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

BlackRock Credit Agreement, which amended certain provisions of the BlackRock Credit Agreement.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for further information on the Vifor Termination Agreement.

3 unchanged sentences

The Initial Warrant and the Tranche C Warrant are liabilities classified under ASC 815, Derivatives and Hedging , as they could potentially require net cash settlement outside of the Company’s control.

The Initial Warrant and the Tranche C Warrant are measured at fair value each period with changes in fair value presented within the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The fair value of the warrant liability was $ 14.2 million and $ 5.2 million as of June 30, 2025 and December 31, 2024, respectively.

The Initial Warrant and the Tranche C Warrant are measured at fair value each reporting period and when a warrant is exercised, with the changes in fair value presented within the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The fair value of the warrant liability was $ 5.2 million as of September 30, 2025 and December 31, 2024.

See Note 3, Fair Value of Financial Instruments , for information on the fair value determination.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 11

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

On July 21, 2025, the Warrant Holder exercised its option to purchase 2,115,384 shares of the Company's common stock under the Initial Warrant on a cashless basis at an exercise price per share of $ 1.30 .

As a result of the cashless exercise, the Company issued 1,408,588 shares to the Warrant Holder under the Initial Warrant.

See Note 17, Subsequent Events , for further information.

A cashless exercise allows the Warrant Holder to convert the warrants into shares of the Company's common stock without the need for a cash payment.

Instead of paying cash upon exercise, the Warrant Holder received a reduced number of shares based on a predetermined formula.

On July 23, 2025, as a result of the cashless exercise, the Company issued 1,408,588 shares to the Warrant Holder under the Initial Warrant.

Other Agreements Accounted for as Debt

5 unchanged sentences

On the Closing Date, using the proceeds from the BlackRock Credit Agreement, the Company paid the then outstanding principal balance on the Pharmakon Term Loans of $ 35.0 million, plus the outstanding interest and a prepayment fee of $ 0.2 million.

During the six months ended June 30, 2024, the Company recorded a debt extinguishment loss of $ 0.5 million.

The Company recognized no interest expense during the three and six months ended June 30, 2025 and immaterial interest expense during the six months ended June 30, 2024, in each case related to the Pharmakon Loan Agreement.

During the nine months ended September 30, 2024, the Company recorded a debt extinguishment loss of $ 0.5 million.

The Company recognized no interest expense during the three and nine months ended September 30, 2025 and immaterial interest expense during the nine months ended September 30, 2024, in each case related to the Pharmakon Loan Agreement.

See Note 7, Indebtedness , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for further details.

5 unchanged sentences

The Vifor License Agreement was structured as a profit share arrangement between the Company and CSL Vifor in which the Company would receive approximately 66 % of the profits, net of certain pre-specified costs.

In addition, CSL Vifor made an upfront payment to the Company of $ 25.0 million in February 2022 in connection with the amendment and restatement of the Vifor License Agreement, which was previously recorded as long-term deferred revenue in the consolidated balance sheets.

In addition, CSL Vifor made an

Akebia Therapeutics, Inc.

| Form 10-Q | Page 12

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

upfront payment to the Company of $ 25.0 million in February 2022 in connection with the amendment and restatement of the Vifor License Agreement, which was previously recorded as long-term deferred revenue in the consolidated balance sheets.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of the Vifor License Agreement.

4 unchanged sentences

The 2017 Shares and 2022 Shares are subject to standstill agreements and are subject to voting agreements.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 12

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

506 promulgated thereunder as the transaction did not involve any public offering within the meaning of Section 4(a)(2) of the Securities Act.

The 2017 Shares and 2022 Shares have not been registered pursuant to the Securities Act of 1933, as amended, or the Securities Act , and were issued and sold in reliance upon the exemption from registration contained in Section 4(a)(2) of the Securities Act and Rule 506 promulgated thereunder as the transaction did not involve any public offering within the meaning of Section 4(a)(2) of the Securities Act.

Vifor Termination Agreement

14 unchanged sentences

On a quarterly basis, the Company reassesses the expected royalty payments.

The annual effective interest rate as of June 30, 2025 was 37.0 % which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense related to the settlement royalties liability of $ 5.4 million and $ 10.8 million for the three and six months ended June 30, 2025, respectively.

The Company did not recognize interest expense related to the settlement royalties liability during the three and six months ended June 30, 2024.

As of June 30, 2025 and December 31, 2024, the balances related to the settlement royalties liability were as follows (in thousands):

June 30, 2025 December 31, 2024

The annual effective interest rate as of September 30, 2025 was 24.6 % which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense related to the settlement royalties liability of $ 3.9 million and $ 14.7 million for the three and nine months ended September 30, 2025,

Akebia Therapeutics, Inc.

| Form 10-Q | Page 13

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

respectively, and $ 4.4 million for the three and nine months ended September 30, 2024.

As of September 30, 2025 and December 31, 2024, the balances related to the settlement royalties liability were as follows (in thousands):

September 30, 2025 December 31, 2024

Current portion (included in accrued expenses and other current liabilities)

8 unchanged sentences

On March 18, 2022, when the $ 40.0 million was received from CSL Vifor, the Company recorded an initial discount on the Working Capital Fund liability and a corresponding deferred gain on the condensed consolidated balance sheet.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 13

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

On May 3, 2024, the Company and CSL Vifor entered into Amendment #1 to the Vifor License Agreement, or the Amendment .

8 unchanged sentences

The deferred gain is amortized to interest income on a straight-line basis over the WCF Royalty Term.

The amortization of the discount was $ 1.2 million and $ 2.3 million for the three and six months ended June 30, 2025, respectively, and $ 0.9 million and $ 1.6 million for the three and six months ended June 30, 2024, respectively.

The amortization of the deferred gain was $ 1.0 million and $ 2.0 million for the three and six months ended June 30, 2025, respectively, and $ 0.8 million and $ 1.7 million for the three and six months ended June 30, 2024, respectively.

As of June 30, 2025 and December 31, 2024, the balances related to the Working Capital Fund liability were as follows (in thousands):

June 30, 2025 December 31, 2024

The amortization of the discount was $ 1.2 million and $ 3.5 million for the three and nine months ended September 30, 2025, respectively, and $ 1.1 million and $ 2.7 million for the three and nine months ended September 30, 2024, respectively.

The amortization of the deferred gain was $ 1.1 million and $ 3.1 million for the three and nine months ended September 30, 2025, respectively, and $ 0.9 million and $ 2.6 million for the three and nine months ended September 30, 2024, respectively.

As of September 30, 2025 and December 31, 2024, the balances related to the Working Capital Fund liability were as follows (in thousands):

September 30, 2025 December 31, 2024

Current portion

7 unchanged sentences

The Royalty Interest Payments are subject to an annual maximum “cap” of $ 13.0 million, after which the Company will receive 85 % of the Royalty Interest Payments for the remainder of that year.

The Royalty Interest Payments are also subject to an aggregate maximum “cap” of $ 150.0 million, after which the Royalty Interest Payments will revert back to the Company.

The Royalty Interest Payments are also subject to an aggregate maximum “cap” of $ 150.0 million, after which the Royalty Interest Payments will revert back to

Akebia Therapeutics, Inc.

| Form 10-Q | Page 14

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company retains the right to receive all potential future regulatory milestones for Vafseo under the MTPC Agreement.

4 unchanged sentences

On a quarterly basis, the Company reassesses the effective interest rate and adjusts the rate prospectively as needed.

The annual effective interest rate as of June 30, 2025 was 0 % and, therefore the Company did not recognize any non-cash interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The annual effective interest rate as of September 30, 2025 was 0 % and, therefore the Company did not recognize any non-cash interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

As a result of its ongoing involvement in the cash flows related to the royalties and sales milestones in the MTPC Territory, the Company will continue to account for these royalties as non-cash royalty revenue which is reflected in license, collaboration and other revenue in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

Akebia Therapeutics, Inc.

| Form 10-Q | Page 14

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company paid royalties to HCR of $ 0.4 million during each of the three months ended June 30, 2025 and 2024 and $ 0.9 million during each of the six months ended June 30, 2025 and 2024.

As of June 30, 2025 and December 31, 2024 the balances were as follows (in thousands):

Liability related to sale of future royalties June 30, 2025 December 31, 2024

The Company paid royalties to HCR of $ 0.5 million during each of the three months ended September 30, 2025 and 2024 and $ 1.4 million during each of the nine months ended September 30, 2025 and 2024.

As of September 30, 2025 and December 31, 2024 the balances were as follows (in thousands):

Liability related to sale of future royalties September 30, 2025 December 31, 2024

Current portion (included in accrued expenses and other current liabilities) $ 2,144 $ 2,039

9 unchanged sentences

In arriving at the operating lease liabilities, the Company applied incremental borrowing rates ranging from 6.65 % to 6.94 %, which were based on the remaining lease term at either the date of adoption of ASC 842 or the effective date of any subsequent lease term extensions.

As of June 30, 2025, the remaining lease term for the Cambridge Lease was 1.2 years.

Operating lease costs were $ 1.2 million and $ 2.5 million for each of the three and six months ended June 30, 2025 and 2024, respectively.

Cash paid for amounts included in the measurement of operating lease liabilities was $ 1.5 million and $ 2.9 million for the three and six months ended June 30, 2025, respectively, and $ 1.4 million and $ 2.9 million for the three and six months ended June 30, 2024, respectively.

The security deposit in connection with the Cambridge Lease is $ 1.7 million in the form of a letter of credit, which is included as restricted cash in other long-term assets in the accompanying unaudited condensed consolidated balance sheets as of June 30, 2025 and December 31, 2024.

As of September 30, 2025, the remaining lease term for the Cambridge Lease was 0.95 years.

Operating lease costs were $ 1.2 million and $ 3.7 million for each of the three and nine months ended September 30, 2025 and 2024, respectively.

Cash paid for amounts included in the measurement of operating lease liabilities was $ 1.5 million and $ 4.4 million for the three and nine months ended September 30, 2025, respectively, and $ 1.4 million and $ 4.3 million for the three and nine months ended September 30, 2024, respectively.

The security deposit in connection with the Cambridge Lease is $ 1.7 million in the form of a letter of credit, which is included as restricted cash in prepaid expenses and other current assets in the accompanying unaudited condensed consolidated balance sheet as of September 30, 2025 and in other long-term assets in the accompanying unaudited condensed consolidated balance sheet as of December 31, 2024.

Future Lease Commitments

Future commitments under the Cambridge Lease are as follows (in thousands):

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Lease Commitments

7 unchanged sentences

The Company and Siegfried entered into a Master Manufacturing Services and Supply Agreement, most recently amended in February 2023, or the Siegfried Agreement , under which the Company has agreed to purchase a minimum quantity of drug substance of Auryxia at a predetermined price.

As of June 30, 2025, the Company is required to purchase a minimum quantity of drug substance for Auryxia annually at a total cost of approximately $ 16.9 million through the end of 2026.

As of September 30, 2025, the Company is required to purchase a minimum quantity of drug substance for Auryxia annually at a total cost of approximately $ 15.3 million through the end of 2026.

The term of the Siegfried Agreement expires on December 31, 2026.

The Siegfried Agreement provides the Company and Siegfried with certain early termination rights.

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The Company regularly reviews its estimate of the excess firm purchase commitment liability which relates to the amount of minimum purchase commitments under the Siegfried Agreement that exceed the current forecast, including review of assumptions of expected future demand and expiry of inventory.

The excess firm commitment liability recorded in other long-term liabilities was $ 3.6 million as of June 30, 2025 and December 31, 2024.

The excess firm commitment liability recorded in other long-term liabilities was $ 3.6 million as of September 30, 2025 and December 31, 2024.

Patheon Manufacturing

1 unchanged sentence

Under the Patheon Agreement, the Company agreed to purchase from Patheon a certain percentage of the estimated global demand for Vafseo drug product based on certain quarterly and annual forecasts provided by the Company.

As of June 30, 2025, the Company has committed to purchase $ 1.1 million of Vafseo drug product from Patheon through the end of 2026, however, as estimated global demand fluctuates, the Company may have additional future obligations under the Patheon Agreement.

As of September 30, 2025, the Company has committed to purchase $ 1.1 million of Vafseo drug product from Patheon through the end of 2026, however, as estimated global demand fluctuates, the Company may have additional future obligations under the Patheon Agreement.

WuXi STA Manufacturing

2 unchanged sentences

Pursuant to the WuXi STA DS Agreement, the Company has agreed to purchase a certain percentage of the global demand for Vafseo drug substance from WuXi STA.

As of June 30, 2025, the Company has no commitments to purchase Vafseo drug substance from WuXi STA, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DS Agreement.

As of September 30, 2025, the Company has committed to purchase $ 69.2 million of Vafseo drug substance from WuXi STA through the end of 2027, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DS Agreement.

Additionally, on February 10, 2021, the Company entered into a Supply Agreement with WuXi STA, which was amended on October 15, 2024, or the WuXi STA DP Agreement , under which WuXi STA will manufacture and supply Vafseo drug product for commercial purposes under a volume-based pricing structure through January 1, 2032.

5 unchanged sentences

In addition, each party has the ability to terminate the WuXi STA DP Agreement upon the occurrence of certain conditions.

As of June 30, 2025, the Company has committed to purchase $ 0.4 million of Vafseo drug product from WuXi STA through the end of 2025, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DP Agreement.

As of September 30, 2025, the Company has committed to purchase $ 0.8 million of Vafseo drug product from WuXi STA through the first quarter

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

of 2026, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DP Agreement.

Esteve - Assigned Supply Agreement

3 unchanged sentences

Although the Esteve Agreement was assigned to MTPC in December 2022, the Company and Esteve have agreed to negotiate the terms of a new commercial supply relationship.

As of June 30, 2025, the Company has committed to purchase $ 7.6 million of Vafseo drug substance from Esteve through the end of 2025.

As of September 30, 2025, the Company has committed to purchase $ 7.6 million of Vafseo drug substance from Esteve through the end of 2025.

BioVectra - Former Manufacturing and Unconditional Purchase Commitments

1 unchanged sentence

On December 22, 2022, the Company and BioVectra entered into a termination agreement, or the BioVectra Termination Agreement , pursuant to which the parties agreed, among other things, to terminate, effective immediately, any and all existing agreements entered into between the parties in connection with the manufacture and supply, by BioVectra to the Company, of Auryxia drug substance.

Under the terms of the BioVectra Termination Agreement, each of the Company and

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BioVectra released one another from all existing and future claims and liabilities and the return of certain materials and documents.

Under the terms of the BioVectra Termination Agreement, each of the Company and BioVectra released one another from all existing and future claims and liabilities and the return of certain materials and documents.

In addition, the Company agreed to pay BioVectra a total of $ 32.5 million consisting of (i) an upfront payment of $ 17.5 million and (ii) six quarterly payments of $ 2.5 million which commenced in April 2024 and were completed in July 2025, totaling $ 15.0 million.

5 unchanged sentences

The discount on the liability balance is being amortized to interest expense using the effective interest rate method over the term of the liability.

The amortization of the discount was $ 0.1 million and $ 0.3 million for the three and six months ended June 30, 2025, respectively, and $ 0.4 million and $ 1.0 million for the three and six months ended June 30, 2024, respectively.

The amortization of the discount was immaterial and $ 0.3 million for the three and nine months ended September 30, 2025, respectively, and $ 0.4 million and $ 1.3 million for the three and nine months ended September 30, 2024, respectively.

License Agreements

6 unchanged sentences

See Note 10, Commitments and Contingencies , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of this license agreement.

The Company incurred royalty payments due to Panion of approximately $ 3.1 million and $ 5.7 million during the three and six months ended June 30, 2025, respectively, and $ 2.5 million and $ 4.3 million during the three and six months ended June 30, 2024, respectively, relating to the Company’s sales of Auryxia in the U.S.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company incurred royalty payments due to Panion of approximately $ 2.7 million and $ 8.4 million during the three and nine months ended September 30, 2025, respectively, and $ 2.1 million and $ 6.4 million during the three and nine months ended September 30, 2024, respectively, relating to the Company’s sales of Auryxia in the U.S.

and Japan Tobacco, Inc.

8 unchanged sentences

The $ 3.0 million upfront payment was charged to research and development expense at acquisition in June of 2021, as it relates to a development stage compound with no alternative future use.

In December 2024, the Company and Cyclerion entered into Amendment #1 to the Cyclerion Agreement, pursuant to which the Company agreed to pay Cyclerion (i) $ 1.25 million, which was paid in December 2024, and (ii) $ 0.5 million on or before September 30, 2025.

In addition, the parties agreed to the reduction of certain development milestones and the increase of certain royalty rates on net sales and sublicense income.

During the year ended December 31, 2024, the Company recorded the $ 1.25 million payment and $ 0.5 million future payment to research and development expense in accordance with ASC 730, Research and Development, as praliciguat remains a development stage compound with no alternative future use.

Furthermore, the only contingency as it relates to the $ 0.5 million payment due on or before September 30, 2025 is the passage of time.

During the year ended December 31, 2024, the Company recorded the $ 1.25 million payment and $ 0.5 million payment to research and development expense in accordance with ASC 730, Research and Development, as praliciguat remains a development stage compound with no alternative future use.

Furthermore, the only contingency as it related to the $ 0.5 million payment made in September 2025 was the passage of time.

Under the Cyclerion Agreement, as amended, Cyclerion is eligible to receive up to an aggregate of $ 198.5 million from the Company in specified development and regulatory milestone payments on a product-by-product basis.

Cyclerion will also be

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

eligible to receive specified commercial milestones as well as tiered royalties ranging from a mid-single-digit percentage to twenty percent of net sales, on a product-by-product basis, and subject to reduction upon expiration of patent rights or the launch of a generic product in the territory.

Cyclerion will also be eligible to receive specified commercial milestones as well as tiered royalties ranging from a mid-single-digit percentage to twenty percent of net sales, on a product-by-product basis, and subject to reduction upon expiration of patent rights or the launch of a generic product in the territory.

Unless earlier terminated, the Cyclerion Agreement will expire on a product-by-product and country-by-country basis upon the expiration of the last royalty term, which ends upon the longest of (i) the expiration of the patents licensed under the Cyclerion Agreement, (ii) the expiration of regulatory exclusivity for such product and (iii) ten years from first commercial sale of such product.

2 unchanged sentences

Other Third-Party Contracts

The Company contracts with various organizations to conduct R&D activities with remaining contract costs to the Company of approximately $ 57.7 million at June 30, 2025.

The Company contracts with various organizations to conduct R&D activities with remaining contract costs to the Company of approximately $ 86.8 million at September 30, 2025.

The scope of the services under these R&D contracts can be modified upon mutual agreement of the parties, and the contracts or scope of services can be cancelled by the Company upon written notice.

8 unchanged sentences

As permitted under Delaware law, the Company may indemnify its officers, directors and employees for certain events or occurrences that happen by reason of their relationship with, or position held at, the Company.

The Company may also be subject to indemnification obligations by law with respect to the actions of its employees under certain circumstances and in certain jurisdictions.

The Company may also be subject to indemnification obligations by law with respect to the actions of its employees under certain circumstances and in

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

certain jurisdictions.

The Company maintains director and officer liability insurance coverage that is intended to cover a portion of amounts that may be due with respect to indemnification after a deductible is met.

Further, the Company is a party to a variety of agreements in the ordinary course of business under which it may be obligated to indemnify third parties with respect to certain matters.

For the three and six months ended June 30, 2025 and 2024, the Company did not experience any losses related to these indemnification obligations, and no claims were outstanding as of June 30, 2025.

For the three and nine months ended September 30, 2025 and 2024, the Company did not experience any losses related to these indemnification obligations, and no claims were outstanding as of September 30, 2025.

The Company does not have any claims related to these indemnification obligations and consequently concluded that the fair value of these obligations is negligible and no related accruals were recorded.

3 unchanged sentences

The Company recognized the following revenue from Vafseo and Auryxia (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

Product 2025 2024 2025 2024

2 unchanged sentences

Total product revenues $ 56,789 $ 35,592 $ 173,041 $ 107,810

(1) Includes the authorized generic version of Auryxia sold and distributed by the Company's authorized generic distribution partner, Mylan Therapeutics, Inc., or AG Partner , during the three and six months ended June 30, 2025.

The following table presents changes in the Company’s contract assets and liabilities related to the Company's sales to its AG Partner (in thousands):

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Six Months Ended June 30, 2025

Nine Months Ended September 30, 2025

Period Additions Deductions Balance

3 unchanged sentences

Deferred revenue $ — $ 8,118 $ ( 5,250 ) $ 2,868

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company recognized the following revenues related to the Company's sales to its AG Partner as a result of changes in the contract asset and contract liability balances in the respective periods (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

Revenue Recognized in the Period:

10 unchanged sentences

Credits/payments made ( 3,151 ) ( 19,395 ) ( 359 ) ( 22,905 )

Balance at June 30, 2025 $ 348 $ 45,168 $ 6,505 $ 52,021

Balance at September 30, 2025 $ 554 $ 59,238 $ 6,471 $ 66,263

(in thousands) Chargebacks

5 unchanged sentences

Credits/payments made ( 6,631 ) ( 36,778 ) ( 4,177 ) ( 47,586 )

Balance at June 30, 2024 $ 1,437 $ 14,733 $ 5,329 $ 21,499

Balance at September 30, 2024 $ 1,343 $ 15,316 $ 4,507 $ 21,166

Chargebacks, discounts and estimated product returns are recorded as a reduction of revenue in the period the related product revenue is recognized in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

1 unchanged sentence

Estimated product returns on product sales that are not expected to be returned within one year are recorded as other long-term liabilities in the unaudited condensed consolidated balance sheets.

Accounts receivable, net related to product sales, was approximately $ 65.4 million and $ 32.4 million as of June 30, 2025 and December 31, 2024, respectively.

Accounts receivable, net related to product sales, was approximately $ 63.2 million and $ 32.4 million as of September 30, 2025 and December 31, 2024, respectively.

LICENSE, COLLABORATION AND OTHER REVENUE

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company recognized the following revenue from its license, collaboration and other revenue agreements (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

Entity Description 2025 2024 2025 2024

5 unchanged sentences

The following tables present changes in the Company’s contract assets and liabilities related to license and other revenue (in thousands):

Six Months Ended June 30, 2025

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Nine Months Ended September 30, 2025

Period Additions Deductions Balance

2 unchanged sentences

$ 2,010 $ 6,577 $ ( 5,527 ) $ 3,060

Six Months Ended June 30, 2024

Contract liability:

Deferred revenue

$ — $ 1,013 $ — $ 1,013

Nine Months Ended September 30, 2024

Period Additions Deductions Balance

5 unchanged sentences

$ 43,296 $ — $ ( 43,296 ) $ —

(1) Excludes accounts receivable related to amounts due to the Company from product sales of Auryxia and Vafseo which are included in the accompanying unaudited condensed consolidated balance sheets as of June 30, 2025 and 2024.

(2) See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for further information.

The Company recognized the following revenues as a result of changes in the contract asset and contract liability balances in the respective periods (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

Revenue Recognized in the Period:

1 unchanged sentence

Deferred revenue — beginning of the period $ — $ — $ — $ —

During each of the three and six months ended June 30, 2025 and 2024, the Company recognized no revenue from performance obligations satisfied in previous periods.

During each of the three and nine months ended September 30, 2025 and 2024, the Company recognized no revenue from performance obligations satisfied in previous periods.

Medice License Agreement

4 unchanged sentences

(ii) tiered royalties ranging from 10 % to 30 % of Medice's annual net sales of Vafseo in the Medice Territory, subject to reduction in certain circumstances.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The royalties will expire on a country-by-country basis upon the latest to occur of (a) the date of expiration of the last-to-expire valid claim of any Company, Medice or joint patent that covers Vafseo in such country in the Medice Territory, (b) the date of expiration of data or regulatory exclusivity for Vafseo in such country in the Medice Territory and (c) the date that is twelve years from first commercial sale of Vafseo in such country in the Medice Territory.

2 unchanged sentences

In this instance, the Company would receive 70 % of the net product margin of any sales of Vafseo in the non-dialysis patient population, unless Medice requests to share the cost of the development necessary to gain approval to market Vafseo for non-dialysis patients in the Medice Territory and the parties agree on alternative financial terms.

If the Company develops Vafseo for non-dialysis patients, the Company has determined that the activities under the Medice License Agreement represent joint operating activities in which both parties are active participants and of which both parties are exposed to significant risks and rewards that are dependent on the success of the activities.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

significant risks and rewards that are dependent on the success of the activities.

Accordingly, if the Company develops Vafseo for non-dialysis patients, the Company will account for the joint activities in accordance with ASC No.

9 unchanged sentences

The remaining $ 1.4 million was withheld by the German Federal Tax Office and was included in prepaid expenses and other current assets as of December 31, 2024 on the audited consolidated balance sheets.

The $ 1.4 million was received during the six months ended June 30, 2025.

The $ 1.4 million was received during the nine months ended September 30, 2025.

Pursuant to the terms of the Medice License Agreement, the up-front payment of $ 10.0 million is non-refundable and non-creditable against any other amount due to the Company and was allocated to the License Performance Obligation, which was satisfied as of the Medice Effective Date.

1 unchanged sentence

In accordance with ASC 606, the Company will recognize sales-based royalties and milestone payments at the later of when the performance obligation is satisfied or the related sales occur.

During the three and six months ended June 30, 2025, the Company recognized immaterial revenue from Medice royalties.

The Company did not recognize any revenue from Medice royalties during the three and six months ended June 30, 2024.

As of June 30, 2025, there were immaterial contract assets, and no accounts receivable, payables or deferred revenue in connection with the Medice License Agreement.

During each of the three and nine months ended September 30, 2025 and 2024, the Company recognized immaterial revenue from Medice royalties.

As of September 30, 2025, there were $ 0.1 million in contract assets, and no accounts receivable, payables or deferred revenue in connection with the Medice License Agreement.

Supply of Drug Product to Medice

1 unchanged sentence

The Company recognizes revenue under this arrangement when risk of loss passes to Medice, delivery has occurred, and Medice has accepted the product.

The Company did not recognize any revenue under the Medice Supply Agreement during the three and six months ended June 30, 2025 or 2024.

The Company did not recognize any revenue under the Medice Supply Agreement during the three and nine months ended September 30, 2025 or 2024.

MTPC Collaboration Agreement

1 unchanged sentence

In addition, the Company supplies Vafseo to MTPC for both clinical and commercial use in the MTPC Territory.

In February 2021, the Company entered into the Royalty Agreement with HCR, whereby the Company sold its right to receive royalties and sales milestones under the MTPC Agreement, subject to certain caps and other terms

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

and conditions.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for additional information and Note 12, License, Collaboration and Other Revenue , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of the MTPC Agreement.

5 unchanged sentences

The Company re-evaluates the transaction price in each reporting period and as uncertain events are resolved or other changes in circumstances occur.

As of June 30, 2025, all development milestones and $ 25.0 million in regulatory milestones have been achieved.

As of September 30, 2025, all development milestones and $ 25.0 million in regulatory

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milestones have been achieved.

No other regulatory milestones have been assessed as probable of being achieved and as a result have been fully constrained.

4 unchanged sentences

The Company recognizes any revenue from MTPC royalties in the period in which the sales occur.

The Company recognized revenue from MTPC royalties of $ 0.5 million and $ 0.9 million during each of the three and six months ended June 30, 2025 and 2024, respectively.

The Company recognized revenue from MTPC royalties of $ 0.5 million during each of the three months ended September 30, 2025 and 2024, and $ 1.3 million and $ 1.4 million during the nine months ended September 30, 2025 and 2024, respectively.

As noted above, in February 2021, the Company entered into the Royalty Agreement, whereby the Company sold its right to receive these royalties and sales milestones under the MTPC Agreement, subject to certain caps and other terms and conditions.

1 unchanged sentence

The revenue is classified as license and other revenue in the accompanying unaudited condensed consolidated statements of operations and comprehensive income (loss).

As of June 30, 2025, there were no accounts receivable, payables or deferred revenue and $ 0.5 million in contract assets recorded in connection with the MTPC Agreement.

As of September 30, 2025, there were no accounts receivable, payables or deferred revenue and $ 0.5 million in contract assets recorded in connection with the MTPC Agreement.

Supply of Drug Product to MTPC

4 unchanged sentences

The Company does not recognize revenue under this arrangement until risk of loss on the drug product passes to MTPC and delivery has occurred and MTPC has accepted the product.

The Company recognized no revenue under the MTPC Supply Agreement during the three and six months ended June 30, 2025 and $ 0.7 million in revenue under the MTPC Supply Agreement during the three and six months ended June 30, 2024.

The Company recognized no revenue under the MTPC Supply Agreement during the three and nine months ended September 30, 2025 and no revenue and $ 0.7 million in revenue under the MTPC Supply Agreement during the three and nine months ended September 30, 2024, respectively.

As of September 30, 2025, there was $ 1.0 million in accounts receivable and $ 1.0 million in deferred revenue recorded in connection with the MTPC Supply Agreement.

JT and Torii Sublicense Agreement

4 unchanged sentences

The Company identified two performance obligations in connection with its obligations under the JT and Torii Sublicense Agreement:

(i) License and Supply Performance

(i) License and Supply Performance Obligation and (ii) Rights to Future Know-How Performance Obligation .

The Company developed a best estimate of the standalone selling price for the Rights to Future Know-How Performance Obligation primarily based on the likelihood that additional intellectual property covered by the license conveyed will be developed during the term of the arrangement and determined it immaterial.

As such, the Company allocated the entire transaction price to the License and Supply Performance Obligation.

The Company recognized license revenue of $ 1.5 million and $ 4.2 million during the three and nine months ended September 30, 2025, respectively, and $ 1.3 million and $ 3.7 million during the three and nine months ended September 30, 2024, respectively, related to royalties earned on net sales of ferric citrate hydrate in Japan under the trade name Riona.

The Company records the associated mid-single digit percentage of net sales royalty expense due to Panion, the licensor of Riona, in the same period as the royalty revenue from JT and Torii is recorded.

Akebia Therapeutics, Inc.

2 unchanged sentences

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Obligation and (ii) Rights to Future Know-How Performance Obligation .

As such, the Company allocated the entire transaction price to the License and Supply Performance Obligation.

The Company recognized license revenue of $ 1.5 million and $ 2.7 million during the three and six months ended June 30, 2025, respectively, and $ 1.3 million and $ 2.5 million during the three and six months ended June 30, 2024, respectively, related to royalties earned on net sales of ferric citrate hydrate in Japan under the trade name Riona.

CAPITAL STOCK

Authorized and Outstanding Capital Stock

As of June 30, 2025, the authorized capital stock of the Company included 350,000,000 shares of common stock, $ 0.00001 par value per share, of which 263,041,832 and 224,848,992 shares were issued and outstanding as of June 30, 2025 and December 31, 2024, respectively;

and 25,000,000 shares of undesignated preferred stock, $ 0.00001 par value per share, of which no shares were issued and outstanding as of June 30, 2025 and December 31, 2024.

As of September 30, 2025, the authorized capital stock of the Company included 350,000,000 shares of common stock, $ 0.00001 par value per share, of which 265,226,038 and 224,848,992 shares were issued and outstanding as of September 30, 2025 and December 31, 2024, respectively;

and 25,000,000 shares of undesignated preferred stock, $ 0.00001 par value per share, of which no shares were issued and outstanding as of September 30, 2025 and December 31, 2024.

At-the-Market Facility

1 unchanged sentence

During the year ended December 31, 2023, the Company sold 6,189,974 shares of common stock under this program with gross proceeds of $ 6.8 million ($ 6.7 million, net of offering expenses).

During the six months ended June 30, 2024, the Company sold 13,261,311 shares of its common stock under this program with gross proceeds of $ 19.2 million ($ 18.7 million, net of offering expenses).

During the nine months ended September 30, 2024, the Company sold 13,261,311 shares of its common stock under this program with gross proceeds of $ 19.2 million ($ 18.7 million, net of offering expenses).

On September 3, 2024, in connection with the filing of a new shelf registration statement on Form S-3, the Company filed a prospectus related to the Company's amended and restated sales agreement (which amended and restated the Original Sales Agreement), with Jefferies, as the Company’s sales agent, pursuant to which the Company is able to offer and sell up to $ 75.0 million of its common stock at current market prices from time to time.

Since September 12, 2024 (the date the Company’s shelf registration statement on Form S-3 went effective) through December 31, 2024, the Company sold 14,271,631 shares of its common stock under this program with gross proceeds of $ 24.3 million ($ 23.8 million, net of offering expenses).

During the six months ended June 30, 2025, the Company sold 9,437,364 shares of its common stock under this program with gross proceeds of $ 18.7 million ($ 18.4 million, net of offering expenses).

During the nine months ended September 30, 2025, the Company sold 9,437,364 shares of its common stock under this program with gross proceeds of $ 18.7 million ($ 18.4 million, net of offering expenses).

Public Offering

7 unchanged sentences

Warrants to Purchase Common Stock

In connection with the BlackRock Credit Agreement, described in more detail in Note 7, Indebtedness , the Company issued a warrant to purchase 3,076,923 shares of the Company’s common stock, at an exercise price per share of $ 1.30 , and upon the borrowing of Tranche C in February 2025, the Company issued additional warrants to purchase 1,153,846 shares of the Company’s common stock at an exercise price per share of $ 1.30 .

Each warrant is exercisable for eight years from the date of issuance.

The warrants and the common stock issuable upon the exercise of such warrants were not registered under the Securities Act and, accordingly, the holder thereof may only sell common stock issued upon exercise of such warrants pursuant to an effective registration statement under the Securities Act covering the resale of those shares, an exemption under Rule 144 under the Securities Act or another applicable exemption under the Securities Act.

The cashless exercise allowed the Warrant Holder to convert the warrants into shares of the Company's common stock without the need for a cash payment.

Instead of paying cash upon exercise, the Warrant Holder received a reduced number of shares based on a predetermined formula.

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

borrowing of Tranche C in February 2025, the Company issued additional warrants to purchase 1,153,846 shares of the Company’s common stock at an exercise price per share of $ 1.30 .

Each warrant is exercisable for eight years from the date of issuance.

As a result of the cashless exercise, the Company issued 1,408,588 shares to the Warrant Holder under the Initial Warrant.

See Note 17, Subsequent Events , for further information.

July 23, 2025, as a result of the cashless exercise, the Company issued 1,408,588 shares to the Warrant Holder under the Initial Warrant.

STOCK-BASED COMPENSATION AND BENEFIT PLAN

Stock-Based Compensation and Benefit Plans

The Company incurred stock-based compensation expenses of $ 2.7 million and $ 4.9 million during the three and six months ended June 30, 2025, respectively, and $ 2.1 million and $ 4.4 million for the three and six months ended June 30, 2024, respectively.

The Company incurred stock-based compensation expenses of $ 3.2 million and $ 8.1 million during the three and nine months ended September 30, 2025, respectively, and $ 1.6 million and $ 6.1 million for the three and nine months ended September 30, 2024, respectively.

Equity Incentive Plans

The following table contains information about the Company's equity plans:

June 30, 2025 December 31, 2024

September 30, 2025 December 31, 2024

Title of Plan Group Eligible Type of Award Granted (or to be Granted) Awards Outstanding Additional Awards Authorized for Grant Awards Outstanding Additional Awards Authorized for Grant

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(3) This table includes inducement awards that are subject to the terms and conditions of the applicable plan but were granted as inducement awards consistent with Nasdaq Listing Rule 5635(c)(4) and not under the applicable plan:

1,089,025 options included as outstanding under the 2014 Plan in the table and 2,556,763 options included as outstanding under the 2023 Plan in the table as of June 30, 2025 and 1,151,127 options included as outstanding under the 2014 Plan and 2,534,775 options included as outstanding under the 2023 Plan in the table as of December 31, 2024.

1,074,082 options included as outstanding under the 2014 Plan in the table and 3,064,976 options included as outstanding under the 2023 Plan in the table as of September 30, 2025 and 1,151,127 options included as outstanding under the 2014 Plan and 2,534,775 options included as outstanding under the 2023 Plan in the table as of December 31, 2024.

(4) On June 10, 2025, the 2023 Plan was amended to increase the number of shares of common stock available for issuance thereunder by 18,900,000 shares.

Common Stock Options and Stock Appreciation Rights

During the six months ended June 30, 2025, the Company issued 3,634,400 options to employees and 375,200 options to directors under the 2023 Plan.

During the nine months ended September 30, 2025, the Company issued 3,634,400 options to employees and 375,200 options to directors under the 2023 Plan.

Options and SARs granted by the Company generally vest over periods of between 12 and 48 months, subject, in each case, to the individual’s continued service through the applicable vesting date.

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Options and SARs generally expire ten years after the date of grant.

The Company also maintains an inducement award program with a share pool that is separate from the Company's equity plans under which inducement awards may be granted consistent with Nasdaq Listing Rule 5635(c)(4).

During the nine months ended September 30, 2025, the Company granted 1,182,176 options to purchase shares of the Company’s common stock to new hires as inducements to such employees entering into employment with the Company, of which 1,133,176 options remained outstanding as of September 30, 2025.

The Company grants annual service-based stock options to employees and directors and SARs to certain executives under the 2023 Plan and previously granted options to employees and directors under the 2014 Plan.

In addition, the Company issues stock options to directors, new hires and occasionally to other employees not in connection with the annual grant process.

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

During the six months ended June 30, 2025, the Company granted 644,413 options to purchase shares of the Company’s common stock to new hires as inducements to such employees entering into employment with the Company, of which 605,213 options remained outstanding as of June 30, 2025.

In addition, the Company issues stock options to directors, new hires and occasionally to other employees not in connection with the annual grant process.

Finally, the Company grants performance-based stock options which generally vest in connection with the achievement of specified commercial, regulatory and corporate milestones.

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The expense recognized for these awards is based on the grant date fair value of the Company’s common stock multiplied by the number of options granted and recognized over time based on the probability of meeting such commercial, regulatory and corporate milestones.

The combined stock option activity for the six months ended June 30, 2025, is as follows:

The combined stock option activity for the nine months ended September 30, 2025, is as follows:

Options Weighted Average Exercise Price Weighted-Average Contractual Life (years) Aggregate Intrinsic Value (in thousands)

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Canceled and forfeited ( 1,126,622 ) $ 1.74 — —

Outstanding at June 30, 2025 19,232,788 $ 3.06 7.09 years $ 28,382

Exercisable at June 30, 2025 10,087,967 $ 4.10 5.38 years —

As of June 30, 2025, there was approximately $ 13.5 million of unrecognized compensation costs related to stock options, which is expected to be recognized over a weighted average period of 2.89 years.

Outstanding at September 30, 2025 18,468,508 $ 2.86 7.29 years $ 15,160

Exercisable at September 30, 2025 9,360,308 $ 3.68 5.84 years $ 7,746

As of September 30, 2025, there was approximately $ 13.5 million of unrecognized compensation costs related to stock options, which is expected to be recognized over a weighted average period of 2.82 years.

Restricted Stock Units

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RSU and PSU activity is as follows:

Akebia Therapeutics, Inc.

| Form 10-Q | Page 25

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

2014 Plan 2023 Plan

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Forfeited and canceled ( 120,409 ) $ 1.05 ( 766,103 ) $ 1.80

Unvested as of June 30, 2025 476,268 $ 0.63 6,439,567 $ 2.08

As of June 30, 2025, there was $ 11.3 million of unrecognized compensation costs related to time-based RSUs and PSUs, which is expected to be recognized over a weighted-average period of 2.08 years.

Unvested as of September 30, 2025 410,733 $ 0.63 6,237,794 $ 2.09

As of September 30, 2025, there was $ 9.7 million of unrecognized compensation costs related to time-based RSUs and PSUs, which is expected to be recognized over a weighted-average period of 1.90 years.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 26

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Employee Stock Purchase Plan

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In addition, an employee may not purchase more than 1,500 shares in any offering period.

As of June 30, 2025 and December 31, 2024, a total of 4,354,707 and 4,448,069 shares of the Company’s common stock were available for future issuance under the ESPP, respectively.

The Company issued 93,362 shares under the ESPP during the six months ended June 30, 2025.

As of September 30, 2025 and December 31, 2024, a total of 4,260,647 and 4,448,069 shares of the Company’s common stock were available for future issuance under the ESPP, respectively.

The Company issued 187,422 shares under the ESPP during the nine months ended September 30, 2025.

Stock-Based Compensation Expense

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The weighted-average assumptions used in calculating the fair values of the rights to acquire stock under the 2023 Plan, the 2014 Plan and inducement awards were as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

Stock Options 2025 2024 2025 2024

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The Company has classified stock-based compensation in its unaudited condensed consolidated statements of operations and comprehensive income (loss) as follows (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

2025 2024 2025 2024

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The following summarizes the calculation of net income (loss) per share:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(Dollars in thousands, except per share amounts) 2025 2024 2025 2024

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Potentially dilutive securities including common stock options, RSUs, SARs and warrants have been excluded from the calculation of diluted net loss per share as their effects would be anti-dilutive.

Therefore, for the three and six months ended June 30, 2024 in which the Company reported a net loss, the weighted average number of shares outstanding used to calculate both basic and diluted net loss per share were the same.

Therefore, for the three and nine months ended September 30, 2024 in which the Company reported a net loss, the weighted average number of shares outstanding used to calculate both basic and diluted net loss per share were the same.

The shares in the table below were excluded from the calculation of diluted net loss per share, prior to the use of the treasury stock method, due to their anti-dilutive effect:

Three and Six Months Ended June 30, 2024

Three and Nine Months Ended September 30, 2024

Warrants 3,076,923

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The measure of segment assets is reported on the consolidated balance sheets as total consolidated assets.

The following table presents information about reported segment revenues, segment profit and significant segment expenses for the three and six months ended June 30, 2025 and 2024:

The following table presents information about reported segment revenues, segment profit and significant segment expenses for the three and nine months ended September 30, 2025 and 2024:

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

2025 2024 2025 2024

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Loss on extinguishment of debt — — — ( 517 )

Net income (loss) before income taxes $ 247 $ ( 8,582 ) $ 6,359 $ ( 26,567 )

Income (loss) before income taxes 1,155 ( 20,039 ) 7,514 ( 46,606 )

Income tax expense ( 615 ) — ( 615 ) —

Net income (loss) $ 540 $ ( 20,039 ) $ 6,899 $ ( 46,606 )

SUBSEQUENT EVENTS

The Company has evaluated events and transactions occurring after the balance sheet date through the filing date of this Form 10-Q with the Securities and Exchange Commission, to ensure that the unaudited condensed consolidated financial statements include appropriate disclosure of events both recognized in the accompanying unaudited condensed consolidated financial statements as of June 30, 2025, and events which occurred subsequently but were not recognized in the consolidated financial statements.

Exercise of Warrants

A cashless exercise allows the Warrant Holder to convert the warrants into shares of the Company's common stock without the need for a cash payment.

Instead of paying cash upon exercise, the Warrant Holder received a reduced number of shares based on a predetermined formula.

On July 23, 2025, as a result of the cashless exercise, the Company issued 1,408,588 shares to the Warrant Holder under the Initial Warrant.

The Company has evaluated events and transactions occurring after the balance sheet date through the filing date of this Form 10-Q with the Securities and Exchange Commission, to ensure that the unaudited condensed consolidated financial statements include appropriate disclosure of events both recognized in the accompanying unaudited condensed consolidated financial statements as of September 30, 2025, and events which occurred subsequently but were not recognized in the consolidated financial statements.

Akebia Therapeutics, Inc.

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Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements