What changed in this filing

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Item 1. Financial Statements

2025-08-07 compared with 2025-05-08 · 295 added, 238 removed, 718 unchanged (43% of the section changed)

2 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED BALANCE SHEETS

(dollars in thousands, except per share amounts) March 31,

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

2025 December 31,

10 unchanged sentences

Total assets $ 345,595 $ 220,670

Liabilities and stockholders' deficit

Liabilities and stockholders' equity (deficit)

Current liabilities:

14 unchanged sentences

Stockholders' equity (deficit):

Preferred stock $ 0.00001 par value, 25,000,000 shares authorized;

no shares issued and

outstanding at March 31, 2025 and December 31, 2024

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

Common stock $ 0.00001 par value;

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

261,644,590 and 224,848,992 shares issued and outstanding at March 31, 2025 and December 31, 2024, respectively

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

Additional paid-in capital 1,701,217 1,629,167

8 unchanged sentences

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

Three Months Ended March 31,

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

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

15 unchanged sentences

Interest expense ( 6,834 ) ( 2,149 ) ( 14,604 ) ( 4,647 )

Other income 213 95

Other income (expense) ( 28 ) ( 39 ) 185 56

Change in fair value of warrant liability ( 6,980 ) 2,331 ( 6,825 ) 2,201

6 unchanged sentences

Diluted $ 0.00 $( 0.04 ) $ 0.02 $( 0.13 )

Weighted average common shares outstanding:

Weighted average shares of common stock outstanding:

Basic 262,565,500 209,705,397 249,106,383 207,330,274

18 unchanged sentences

Balance at March 31, 2024 209,454,149 $ 2 $ 1,599,669 $ 6 $ ( 1,626,935 ) $ ( 27,258 )

Exercise of options 23,892 — 14 — — 14

Stock-based compensation expense — — 2,072 — — 2,072

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

— — — — ( 8,582 ) ( 8,582 )

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

Common Stock Additional Paid-In

1 unchanged sentence

Deficit Total Stockholders'

(Deficit) Equity

Equity (Deficit)

(dollars in thousands) Shares Amount

7 unchanged sentences

Restricted stock unit vesting 1,660,547 — — — — —

— — — — 6,112 6,112

Net income — — — — 6,112 6,112

Balance at March 31, 2025 261,644,590 $ 2 $ 1,696,821 $ 6 $ ( 1,672,248 ) $ 24,581

Issuance of common stock, net of

issuance costs 850,000 — 1,542 — — 1,542

Exercise of options 95,996 — 178 — — 178

Stock-based compensation expense — — 2,676 — — 2,676

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

— — — — 247 247

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

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

3 unchanged sentences

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Three Months Ended March 31,

Six Months Ended June 30,

(dollars in thousands) 2025 2024

11 unchanged sentences

Write-down of inventory 115 1,061

Change in excess inventory purchase commitments — 2,068

Gain on the sale of property and equipment ( 172 ) —

10 unchanged sentences

Other long-term liabilities 605 ( 3,478 )

Net cash used in operating activities ( 13,587 ) ( 19,432 )

Net cash provided by (used in) operating activities 8,758 ( 29,498 )

Investing Activities:

39 unchanged sentences

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

As of March 31, 2025, the Company had cash and cash equivalents of approximately $ 113.4 million.

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

7 unchanged sentences

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 months ended March 31, 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 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.

Basis of Presentation and Principles of Consolidation

21 unchanged sentences

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 March 31, 2025, cash and cash equivalents primarily included cash on hand.

As of June 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.

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

(in thousands) March 31, 2025 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

Cash and cash equivalents $ 137,308 $ 51,870

9 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 $ 1.9 million and $ 1.2 million as of March 31, 2025 and December 31, 2024, respectively.

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 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

Three Months Ended March 31,

Six Months Ended June 30,

Beginning balance $ 1,212 $ 1,029

21 unchanged sentences

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):

March 31, 2025

June 30, 2025

Level 1 Level 2 Level 3 Total Fair Value

Cash equivalents:

Money market funds $ 117,868 $ — $ — $ 117,868

Long-term liability:

4 unchanged sentences

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

Warrant liability – The warrant liability is classified within Level 2 of the fair value hierarchy because it is valued using inputs which are observable either directly or indirectly.

The fair value was calculated using the Black-Scholes option pricing model using the following key inputs:

volatility, risk-free rate, dividend yield and expected term.

Akebia Therapeutics, Inc.

2 unchanged sentences

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.

Warrant liability – The warrant liability is classified within Level 2 of the fair value hierarchy because it is valued using inputs which are observable either directly or indirectly.

The fair value was calculated using the Black-Scholes option pricing model using the following key inputs:

volatility, risk-free rate, dividend yield and expected term.

Inventories consists of the following (in thousands):

March 31, 2025 December 31, 2024

June 30, 2025 December 31, 2024

Inventories, current:

7 unchanged sentences

Total inventories $ 58,570 $ 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) totaled approximately $ 0.2 million and $ 0.6 million during the three months ended March 31, 2025 and 2024, respectively.

For the three months ended March 31, 2024, the Company realized lower cost of product and other revenue of $ 3.7 million 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 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.

INTANGIBLE ASSET AND GOODWILL

4 unchanged sentences

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

The Company recorded $ 9.0 million in amortization expense for the three months ended March 31, 2024 related to the developed product rights for Auryxia.

As of each of March 31, 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 $ 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 has not identified any goodwill impairment to date.

1 unchanged sentence

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

Description March 31, 2025 December 31, 2024

Description June 30, 2025 December 31, 2024

Prepaid manufacturing $ — $ 4,029

3 unchanged sentences

Such amounts are reclassified to work-in-process inventory upon the quality release of the batches and transfer of title to the Company from the CMO.

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 March 31, 2025 December 31, 2024

Description June 30, 2025 December 31, 2024

Long-term inventories $ 41,862 $ 34,953

3 unchanged sentences

See Note 4, Inventories , for further information on long-term inventories.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 9

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

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

March 31, 2025 December 31, 2024

Product revenue allowances $ 27,451 $ 15,727

June 30, 2025 December 31, 2024

Product revenue allowances excluding rebates $ 11,416 $ 9,657

Product rebates 33,752 6,070

Product return reserves, current portion 5,132 5,295

14 unchanged sentences

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 .

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;

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);

(ii) Tranche B — $ 8.0 million was funded on April 19, 2024, or the Tranche B Closing Date , and (iii) Tranche C — $ 10.0 million was funded on February 3, 2025, or the Tranche C Closing Date , collectively the Term Loans .

6 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 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) 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 March 31, 2025, the Company's interest rate was 11.07 %.

The Company recognized interest expense related to the BlackRock Credit Agreement of $ 2.1 million and $ 1.0 million during the three months ended March 31, 2025 and 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.

The Term Loan Facility also includes transaction fees ranging from 1.00 % to 1.25 % of the draw down amount as well exit fees of 0.75 % of the amount funded to the relevant tranche.

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.

2 unchanged sentences

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

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.

The Term Loan Facility also includes transaction fees ranging from 1.00 % to 1.25 % of the draw down amount as well as exit fees of 0.75 % of the amount funded to the relevant tranche.

If the Company prepays the outstanding loan prior to maturity, it will be required to pay a prepayment fee ranging from 1.0 % to 4.0 % of the amount prepaid.

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 March 31, 2025, future principal payments under the BlackRock Credit Agreement are as follows (in thousands):

As of June 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 Vifor Termination and Settlement Agreement, or the Vifor Termination Agreement , the Company and Kreos entered into a First Amendment to the BlackRock Credit Agreement, or the BlackRock Credit Amendment , which amended certain provisions of the BlackRock Credit Agreement.

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.

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.

4 unchanged sentences

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 $ 7.2 million and $ 5.2 million as of March 31, 2025 and December 31, 2024, respectively.

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.

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.

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 three months ended March 31, 2024, the Company recorded a debt extinguishment loss of $ 0.5 million.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 11

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company recognized no interest expense and immaterial interest expense related to the Pharmakon Loan Agreement during the three months ended March 31, 2025 and 2024, respectively.

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.

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

11 unchanged sentences

The $ 18.3 million, which represented the premium over the closing stock price, or $ 4.7 million for the 2017 Shares and $ 13.6 million for the 2022 Shares, was previously recorded as long-term deferred revenue in the consolidated balance sheets as it represented consideration related to the Vifor License Agreement.

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

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.

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.

Vifor Termination Agreement

7 unchanged sentences

If the Company exercises the Royalty Buy-Down Option, the WCF Royalty Payments, as described below, will continue as described below.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 12

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The WCF Royalty Payments, as described below, the Settlement Royalty Payments and the Royalty Buy-Down Option are in consideration for the termination of the Vifor License Agreement and all obligations thereunder, and the covenants and agreements set forth in the Vifor Termination Agreement, including the settlement and release of all disputes and claims arising from the Vifor License Agreement.

5 unchanged sentences

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

The annual effective interest rate as of March 31, 2025 was 41.0 % which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense of $ 5.4 million for the three months ended March 31, 2025.

The Company did not recognize interest expense related to the settlement royalties liability during the three months ended March 31, 2024.

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

March 31, 2025 December 31, 2024

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

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 .

Pursuant to the Amendment, and as modified by the Vifor Termination Agreement, the Company and CSL Vifor agreed to modify the method of repayment of the Working Capital Fund such that the Working Capital Fund will be repaid through quarterly tiered royalty payments ranging from 8 % to 14 % of the Company's net sales of Vafseo in the U.S., or the WCF Royalty Payments .

The WCF Royalty Payments will commence on July 1, 2025, and will continue until the earlier of (i) the cumulative total of the WCF Royalty Payments equals $ 40.0 million, or (ii) May 31, 2028, or the WCF Royalty Term .

The WCF Royalty Payments commenced on July 1, 2025, and will continue until the earlier of (i) the cumulative total of the WCF Royalty Payments equals $ 40.0 million, or (ii) May 31, 2028, or the WCF Royalty Term .

The WCF Royalty Payments are subject to minimum true-up milestones of $ 10.0 million, $ 20.0 million and $ 40.0 million, or the WCF Royalty True-Up Payments , on each of May 31, 2026, May 31, 2027 and May 31, 2028, respectively, or the WCF Royalty True-Up Dates .

5 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 $ 1.1 million and $ 0.7 million for the three months ended March 31, 2025 and 2024,

Akebia Therapeutics, Inc.

| Form 10-Q | Page 13

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

respectively.

The amortization of the deferred gain was $ 1.0 million and $ 0.9 million for the three months ended March 31, 2025 and 2024, respectively.

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

March 31, 2025 December 31, 2024

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

Current portion

5 unchanged sentences

Liability Related to Sale of Future Royalties

On February 25, 2021, the Company entered into a royalty interest acquisition agreement, or the Royalty Agreement , with HealthCare Royalty Partners IV, L.P., or HCR , pursuant to which the Company sold to HCR its right to receive royalties and sales milestones for Vafseo in Japan and certain other Asian countries, such countries collectively, the MTPC Territory , and such payments collectively the Royalty Interest Payments , in each case, payable to the Company under the MTPC Agreement.

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.

6 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 March 31, 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 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).

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).

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 Royalty Agreement.

The Company paid $ 0.5 million and $ 0.4 million of royalties to HCR during the three months ended March 31, 2025 and 2024, respectively.

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

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

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

Current portion (included in accrued expenses and other current liabilities) $ 2,152 $ 2,039

8 unchanged sentences

The Cambridge Lease does not contain residual value guarantees.

In arriving at the operating lease liabilities, the Company applied incremental borrowing rates ranging from 6.65 % to 6.94 %,

Akebia Therapeutics, Inc.

| Form 10-Q | Page 14

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

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 March 31, 2025, the remaining lease term for the Cambridge Lease was 1.45 years.

Operating lease costs were $ 1.2 million for each of the three months ended March 31, 2025 and 2024.

Cash paid for amounts included in the measurement of operating lease liabilities was $ 1.5 million and $ 1.4 million for the three months ended March 31, 2025 and 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 March 31, 2025 and December 31, 2024.

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.

Future Lease Commitments

9 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 March 31, 2025, the Company is required to purchase a minimum quantity of drug substance for Auryxia annually at a total cost of approximately $ 15.6 million through the end of 2026.

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.

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 March 31, 2025 and December 31, 2024.

The excess firm commitment liability recorded in other long-term liabilities was $ 3.6 million as of June 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 March 31, 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 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.

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 March 31, 2025, the Company has committed to purchase $ 6.1 million of Vafseo drug substance from WuXi STA through the first half of 2025, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DS Agreement.

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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.

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 March 31, 2025, the Company has committed to purchase $ 0.9 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 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.

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 March 31, 2025, the Company has committed to purchase $ 7.6 million of Vafseo drug substance from Esteve through the end of 2025.

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.

BioVectra - Former Manufacturing and Unconditional Purchase Commitments

Under the Manufacture and Supply Agreement with BioVectra, Inc., or BioVectra , and the Amended and Restated Product Manufacture and Supply and Facility Construction Agreement with BioVectra, the Company agreed to purchase minimum quantities of Auryxia drug substance annually at predetermined prices as well as reimburse BioVectra for certain costs in connection with construction of a new facility for the manufacture and supply of Auryxia drug substance.

On December 22, 2022, the Company and BioVectra entered into a termination agreement, or 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 BioVectra have 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, totaling $ 15.0 million.

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.

The upfront payment of $ 17.5 million was made during the quarter ended December 31, 2022 and was recognized to cost of product and other revenue.

4 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 $ 0.2 million and $ 0.5 million for the three months ended March 31, 2025 and 2024, respectively.

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.

License Agreements

Panion License Agreement

On April 17, 2019, the Company and Panion & BF Biotech, Inc., or Panion , entered into a second amended and restated license agreement, or Panion Amended License Agreement , which amended and restated in full the license agreement between the Company and Panion.

On April 17, 2019, the Company and Panion & BF Biotech, Inc., or Panion , entered into a second amended and restated license agreement, or the Panion Amended License Agreement , which amended and restated in full the license agreement between the Company and Panion.

The Panion Amended License Agreement provides the Company with an exclusive license under Panion-owned know-how and patents with the right to sublicense, develop, make, use, sell, offer for sale, import and export ferric citrate worldwide, excluding certain Asian-Pacific countries, or the Licensor Territory .

The Panion Amended License Agreement also provides Panion with an exclusive license under the Company-owned patents, with the right to

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

sublicense (with the Company’s written consent), develop, make, use, sell, offer for sale, import and export ferric citrate in certain countries in the Licensor Territory.

The Panion Amended License Agreement also provides Panion with an exclusive license under the Company-owned patents, with the right to sublicense (with the Company’s written consent), develop, make, use, sell, offer for sale, import and export ferric citrate in certain countries in the Licensor Territory.

Under the Panion Amended License Agreement, Panion is eligible to receive from the Company or any sublicensee royalty payments based on a mid-single digit percentage of sales of ferric citrate in the Company’s licensed territories.

1 unchanged sentence

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 $ 2.6 million and $ 1.9 million during the three months ended March 31, 2025 and 2024, respectively, relating to the Company’s sales of Auryxia in the U.S.

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.

and Japan Tobacco, Inc.

1 unchanged sentence

Cyclerion Agreement

In June 2021, the Company entered into a license agreement, or Cyclerion Agreement , with Cyclerion Therapeutics Inc., or Cyclerion , under which the Company obtained an exclusive global license under certain intellectual property rights to research, develop and commercialize praliciguat, an investigational oral soluble guanylate cyclase stimulator.

In June 2021, the Company entered into a license agreement, or the Cyclerion Agreement , with Cyclerion Therapeutics Inc., or Cyclerion , under which the Company obtained an exclusive global license under certain intellectual property rights to research, develop and commercialize praliciguat, an investigational oral soluble guanylate cyclase stimulator.

Under the terms of the Cyclerion Agreement, the Company made an upfront payment of $ 3.0 million to Cyclerion, which was paid during the second quarter of 2021.

4 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 License Agreement, or the Cyclerion Amendment , 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 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.

2 unchanged sentences

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 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

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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 $ 42.2 million at March 31, 2025.

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

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 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.

In some instances, the contracts may be cancelled by the third party upon written notice.

4 unchanged sentences

Changes in the Company’s estimates could have a material impact and are recorded as litigation progresses and new information comes to light.

Although the outcomes of

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potential legal proceedings are inherently difficult to predict, the Company does not expect the resolution of current legal proceedings to have a material adverse effect on its financial position, results of operations or cash flows of the Company.

Although the outcomes of potential legal proceedings are inherently difficult to predict, the Company does not expect the resolution of current legal proceedings to have a material adverse effect on its financial position, results of operations or cash flows.

Guarantees and Indemnifications

3 unchanged sentences

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 months ended March 31, 2025 and 2024, the Company did not experience any losses related to these indemnification obligations, and no claims were outstanding as of March 31, 2025.

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.

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 March 31,

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

Product 2025 2024 2025 2024

Vafseo $ 13,279 $ — $ 25,313 $ —

47,183 41,209 90,939 72,218

Total product revenues $ 60,461 $ 41,209 $ 116,252 $ 72,218

$ 55,791 $ 31,009

(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 months ended March 31, 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):

Three Months Ended March 31, 2025

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Six Months Ended June 30, 2025

Period Additions Deductions Balance

1 unchanged sentence

Accounts receivable $ — $ 8,662 $ ( 3,294 ) $ 5,368

$ — $ 1,241 $ — $ 1,241

Contract liabilities:

Deferred revenue $ — $ 8,118 $ ( 2,586 ) $ 5,532

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,

Revenue Recognized in the Period:

2025 2024 2025 2024

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Deferred revenue — beginning of the period

$ 1,241 $ — $ — $ —

Product revenue allowance and reserve categories were as follows:

6 unchanged sentences

Credits/payments made ( 2,359 ) ( 13,227 ) ( 269 ) ( 15,855 )

Balance at March 31, 2025 $ 496 $ 27,451 $ 6,520 $ 34,467

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

(in thousands) Chargebacks

and Discounts Rebates, Fees

Deductions Product Returns Total

Product Returns Total

Balance at December 31, 2023 $ 1,607 $ 22,991 $ 6,916 $ 31,514

2 unchanged sentences

Credits/payments made ( 4,301 ) ( 27,530 ) ( 3,352 ) ( 35,183 )

Balance at March 31, 2024 $ 1,208 $ 13,564 $ 5,798 $ 20,570

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

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 $ 60.0 million and $ 32.4 million as of March 31, 2025 and December 31, 2024, respectively.

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.

LICENSE, COLLABORATION AND OTHER REVENUE

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

Three Months Ended March 31,

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

Entity Description 2025 2024 2025 2024

Medice License and royalties related to the sale of Vafseo in the EU

$ 16 $ — $ 24 $ —

MTPC License and Product Supply of Vafseo in Japan 502 1,169 870 1,581

2 unchanged sentences

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

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Three Months Ended March 31, 2025

Six Months Ended June 30, 2025

Period Additions Deductions Balance

2 unchanged sentences

$ 2,010 $ 3,556 $ ( 3,521 ) $ 2,045

Three Months Ended March 31, 2024

Six Months Ended June 30, 2024

Period Additions Deductions Balance

5 unchanged sentences

$ 43,296 $ 695 $ ( 695 ) $ 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 March 31, 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 March 31,

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

Revenue Recognized in the Period:

2025 2024 2025 2024

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

During each of the three months ended March 31, 2025 and 2024, the Company recognized no revenue from performance obligations satisfied in previous periods.

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.

Medice License Agreement

On May 24, 2023, or Medice Effective Date , the Company and MEDICE Arzneimittel Pütter GmbH & Co.

KG, or Medice , entered into a License Agreement, or the Medice License Agreement , pursuant to which the Company granted to Medice an exclusive license to develop and commercialize Vafseo for the treatment of anemia in adult patients with CKD in the European Economic Area, the United Kingdom, Switzerland and Australia, or collectively the Medice Territory .

On May 24, 2023, or the Medice Effective Date , the Company and MEDICE Arzneimittel Pütter GmbH & Co.

KG, or Medice , entered into a License Agreement, or the Medice License Agreement , pursuant to which the Company granted to Medice an exclusive license to develop and commercialize Vafseo for the treatment of anemia in adult patients with CKD in the EEA, the UK, Switzerland and Australia, or collectively the Medice Territory .

Under the Medice License Agreement, the Company received an up-front payment of $ 10.0 million and is eligible to receive the following payments:

1 unchanged sentence

(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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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.

4 unchanged sentences

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

808, Collaborative

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Arrangements , or ASC 808 .

808, Collaborative Arrangements , or ASC 808 .

Additionally, the Company has determined that in the context of the development of Vafseo for non-dialysis patients, Medice does not represent a customer as contemplated by ASC 606.

7 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 three months ended March 31, 2025.

The $ 1.4 million was received during the six months ended June 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 months ended March 31, 2025, the Company recognized immaterial revenue from Medice royalties.

The Company did not recognize any revenue from Medice royalties during the three months ended March 31, 2024.

As of March 31, 2025, there were immaterial contract assets, and no accounts receivable, payables or deferred revenue in connection with the Medice License Agreement.

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.

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 months ended March 31, 2025 or 2024.

The Company did not recognize any revenue under the Medice Supply Agreement during the three and six months ended June 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 and conditions.

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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 March 31, 2025, all development milestones and $ 25.0 million in regulatory milestones have been achieved.

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

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

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The Company allocates the transaction price to each performance obligation based on the Company’s best estimate of the relative standalone selling price.

3 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 $ 0.4 million during each of the three months ended March 31, 2025 and 2024.

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.

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 March 31, 2025, there were no accounts receivable, payables or deferred revenue and $ 0.4 million in contract assets recorded in connection with the MTPC Agreement.

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.

Supply of Drug Product to MTPC

On July 15, 2020, the Company and MTPC entered into a supply agreement, or the MTPC Supply Agreement , under which the Company supplies Vafseo drug product to MTPC for commercial use in Japan and certain other Asian countries, as contemplated by the MTPC Agreement.

See 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 this supply agreement.

On December 16, 2022, the Company, MTPC and Esteve executed an Assignment of Supply Agreement, or the Esteve Assignment Agreement , pursuant to which the rights and obligations of the Company under the Esteve Agreement were transferred to MTPC.

The Company has no further obligation to take delivery of, or pay for, product delivered by Esteve except as disclosed in Note 10, Commitments and Contingencies .

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.

JT and Torii Sublicense Agreement

The Company has an Amended and Restated Sublicense Agreement, which was amended in June 2013, with JT and Torii, or JT and Torii Sublicense Agreement , under which JT and Torii obtained the exclusive sublicense rights for the development and commercialization of ferric citrate hydrate in Japan.

The Company has an Amended and Restated Sublicense Agreement, which was amended in June 2013, with JT and Torii, or the JT and Torii Sublicense Agreement , under which JT and Torii obtained the exclusive sublicense rights for the development and commercialization of ferric citrate hydrate in Japan.

JT and Torii are responsible for the future development and commercialization costs in Japan.

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

(i) License and Supply Performance

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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 $ 1.2 million during each of the three months ended March 31, 2025 and 2024 related to royalties earned on net sales of ferric citrate hydrate in Japan under the trade name Riona.

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.

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.

1 unchanged sentence

Authorized and Outstanding Capital Stock

As of March 31, 2025, the authorized capital stock of the Company included 350,000,000 shares of common stock, $ 0.00001 par value per share, of which 261,644,590 and 224,848,992 shares were issued and outstanding as of March 31, 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 March 31, 2025 and December 31, 2024.

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.

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 three months ended March 31, 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 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).

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

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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 three months ended March 31, 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).

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).

Public Offering

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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 .

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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.

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.

STOCK-BASED COMPENSATION AND BENEFIT PLAN

Stock-Based Compensation and Benefit Plans

The Company incurred stock-based compensation expenses of $ 2.2 million and $ 2.4 million for the three months ended March 31, 2025 and 2024, respectively.

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.

Equity Incentive Plans

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

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March 31, 2025 December 31, 2024

June 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

Keryx Equity Plans (1)(2)

Employees, directors and consultants Stock options and RSUs 153,346 — 163,765 —

Employees, directors and consultants Stock options and restricted stock units ( RSUs )

153,346 — 163,765 —

Akebia Therapeutics, Inc.

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(the 2014 Plan )

Employees, directors, consultants and advisors Stock options, RSUs, SARs and performance awards 10,314,595 — 11,559,708 —

Employees, directors, consultants and advisors Stock options, RSUs, stock appreciation rights ( SARs ) and performance awards

9,982,813 — 11,559,708 —

Akebia Therapeutics, Inc.

2023 Stock Incentive Plan (3) ( the 2023 Plan )

2023 Stock Incentive Plan, as amended (3) (4) (the 2023 Plan )

(replaced 2014 Plan)

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(1) The Keryx Equity Plans consist of the Keryx Biopharmaceuticals, Inc.

1999 Share Option Plan, Keryx Biopharmaceuticals, Inc., as amended, the 2004 Long-Term Incentive Plan, as amended, the Keryx Biopharmaceuticals, Inc.

1999 Share Option Plan, as amended, the 2004 Long-Term Incentive Plan, as amended, the Keryx Biopharmaceuticals, Inc.

2007 Incentive Plan, the Keryx Biopharmaceuticals Inc.

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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:

1,120,196 options included as outstanding under the 2014 Plan in the table and 2,274,138 options included as outstanding under the 2023 Plan in the table as of March 31, 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.

1,089,025 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.

(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 three months ended March 31, 2025, the Company issued 3,634,400 options to employees under the 2023 Plan.

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.

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.

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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 three months ended March 31, 2025, the Company granted 217,613 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 211,088 options remained outstanding as of March 31, 2025.

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

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.

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.

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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.

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The combined stock option activity for the three months ended March 31, 2025, is as follows:

The combined stock option activity for the six months ended June 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 ( 1,105,629 ) $ 1.74 — —

Outstanding at March 31, 2025

19,102,010 $ 3.01 7.54 years $ 6,152

Exercisable at March 31, 2025

9,208,835 $ 4.40 5.92 years —

As of March 31, 2025, there was approximately $ 13.2 million of unrecognized compensation costs related to stock options, which is expected to be recognized over a weighted average period of 3.17 years.

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.

Restricted Stock Units

Generally, restricted stock units, or RSUs , granted by the Company vest in one of the following ways:

Generally, RSUs granted by the Company vest in one of the following ways:

(i) 100 % of each RSU grant vests on the first anniversary of the grant date, (ii) one third of each RSU grant vests on the first, second and third anniversaries of the grant date, or (iii) one third of each RSU grant vests on the first anniversary of the grant date and the remaining two thirds vests in eight substantially equal quarterly installments beginning after the one year anniversary, subject, in each case, to the individual’s continued service through the applicable vesting date.

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RSU and PSU activity is as follows:

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2014 Plan 2023 Plan

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Forfeited and canceled ( 116,309 ) $ 1.06 ( 700,153 ) $ 1.76

Unvested as of March 31, 2025

741,969 $ 0.76 6,716,706 $ 1.94

As of March 31, 2025, there was $ 12.2 million of unrecognized compensation costs related to time-based RSUs and PSUs, which is expected to be recognized over a weighted-average period of 2.38 years.

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.

Employee Stock Purchase Plan

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Under the ESPP, substantially all employees may voluntarily enroll to purchase shares of the Company’s common stock through payroll deductions at a price equal to 85 % of the lower of the fair market values of the stock as of the beginning or the end of the six-month offering period.

An employee's payroll deductions under the ESPP are limited to 15 % of the

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

employee's compensation, and an employee may not purchase more than $ 25,000 worth of stock during any calendar year.

An employee's payroll deductions under the ESPP are limited to 15 % of the employee's compensation, and an employee may not purchase more than $ 25,000 worth of stock during any calendar year.

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

As of March 31, 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 three months ended March 31, 2025.

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.

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 March 31,

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

Stock Options 2025 2024 2025 2024

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Expected volatility 111.61 % - 123.58 % 109.98 % - 118.61 % 111.61 % - 123.58 % 109.98 % - 118.61 %

Expected term (years) 6.25 years - 6.25 years 6.25 years - 6.25 years

Expected term (years) 5.51 years - 6.25 years 5.51 years - 6.25 years 5.51 years - 6.25 years 5.51 years - 6.25 years

Expected dividend yield — % — % — % — %

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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 March 31,

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

2025 2024 2025 2024

Cost of goods sold $ 183 $ 83 $ 322 $ 169

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Total stock-based compensation $ 2,676 $ 2,072 $ 4,863 $ 4,432

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

NET INCOME (LOSS) PER SHARE

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

For periods in which the Company reports a net loss, the weighted average number of shares outstanding used to calculate both basic and diluted net loss per share were the same except for the three months ended March 31, 2025, as the Company had net income for that period.

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

Three Months Ended March 31,

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

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

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

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

Denominator for basic net income (loss) per share - weighted average outstanding shares of common stock 262,565,500 209,705,397 249,106,383 207,330,274

Dilutive effect of common stock options and SARs 3,355,271 — 2,899,471 —

Dilutive effect of RSUs 2,959,976 — 2,688,180 —

Dilutive effect of warrants 2,215,180 — 1,836,580 —

Dilutive effect of ESPP 8,093 — 8,451 —

Denominator for diluted net income (loss) per share - weighted average outstanding shares of common stock and assumed conversions 271,104,020 209,705,397 256,539,065 207,330,274

Basic net income (loss) per share $ 0.00 $ ( 0.04 ) $ 0.03 $ ( 0.13 )

Diluted net income (loss) per share $ 0.00 $ ( 0.04 ) $ 0.02 $ ( 0.13 )

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.

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

Warrants 3,076,923

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Unvested RSUs 5,963,769

Unvested PSUs 350,500 —

Stock appreciation rights 635,313

Total 26,319,512

(1) The Company granted the Underwriters a 30-day option to purchase up to 3,750,000 additional shares of common stock at the public offering price per share.

These shares are excluded from this table.

See Note 13, Capital Stock , for more information.

SEGMENT INFORMATION

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The accounting policies of the segment are the same as those described in the summary of significant accounting policies.

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The determination of a single business segment is consistent with the consolidated financial information regularly reviewed by the chief executive officer, who is the Company's chief operating decision maker, or CODM , in assessing segment performance and deciding how to allocate resources on a consolidated basis.

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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 months ended March 31, 2025 and 2024:

Three Months Ended March 31,

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:

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

2025 2024 2025 2024

Revenues $ 62,472 $ 43,648 $ 119,808 $ 76,255

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Panion royalty 3,093 2,478 5,658 4,331

Excess firm purchase commitment charge — 2,068 — 2,068

Amortization of intangible asset — 9,011 — 18,021

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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 disclose of events both recognized in the accompanying unaudited condensed consolidated financial statements as of March 31, 2025, and events which occurred subsequently but were not recognized in the consolidated financial statements.

The Company has concluded that no subsequent events have occurred that require disclosure.

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.

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