What changed in this filing

/stocks — the workspaceLOADING

Item 2. Management’s Discussion and Analysis

2025-08-07 compared with 2025-05-08 · 188 added, 97 removed, 287 unchanged (50% of the section changed)

21 unchanged sentences

The current U.S.

market opportunity for the treatment of anemia due to CKD in patients with dialysis is approximately $1 billion based on current ESA pricing and Vafseo is the only oral HIF-based treatment available in the U.S.

market opportunity for the treatment of anemia due to CKD in patients with dialysis is approximately $1 billion based on current erythropoiesis stimulating agent, or ESA, pricing and Vafseo is the only oral HIF-based treatment available in the U.S.

We are committed to pursuing a path for label expansion for Vafseo for CKD non-dialysis dependent patients.

We continue to work towards our goal to initiate VALOR, a Phase 3 cardiovascular outcome study of approximately 1,500 U.S.

subjects with late-stage CKD anemia not on dialysis with a comparator to ESA, by the end of 2025 and recently requested a Type-C meeting with the FDA.

The study will be one part of what we believe will be a robust data package that will likely include data from the 1,700 U.S.

patients in the global Phase 3 PRO 2 TECT program, as well as safety data from the commercial use of Vafseo in the U.S.

in dialysis patients, and data on the use of Vafseo in Japan in dialysis and non-dialysis patients where Vafseo has been in the market since 2020.

In the European Union, or EU , the United Kingdom, or UK , Switzerland and Australia, Vafseo is approved for the treatment of symptomatic anemia associated with CKD in adults on chronic maintenance dialysis.

10 unchanged sentences

In March 2025, Auryxia lost exclusivity, or LoE .

We believe the dynamics of Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE situations, but the impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

Ferric citrate hydrate has also been approved in Japan, and is marketed and sold by our Japanese sublicensee, Japan Tobacco, Inc., and its subsidiary, Torii Pharmaceutical Co., Ltd., collectively, JT and Torii , as an oral treatment for the improvement of hyperphosphatemia in patients with CKD, including DD-CKD and NDD-CKD, and for the treatment of

We believe the dynamics of

Akebia Therapeutics, Inc.

| Form 10-Q | Page 29

adult patients with IDA under the trade name as Riona in Japan.

Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE situations, but the impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

Averoa SAS, or Averoa , has an exclusive license to develop and commercialize ferric citrate in the European Economic Area, or EEA , Turkey, Switzerland, the UK, the Balkans and certain countries in Eastern Europe and the Middle East.

1 unchanged sentence

In March 2025, the Committee for Medicinal Products for Human Use of the European Medicines Agency adopted a positive opinion recommending the European Commission, or EC , to approve Averoa’s marketing authorization.

The final EC decision is expected on June 1, 2025.

The EC granted marketing authorization in June 2025.

Our HIF-based product candidates and other pipeline assets are being evaluated to target areas of unmet needs.

13 unchanged sentences

that protected us from generic drug competition until March 20, 2025.

Following LoE, in March 2025, our AG Partner began to sell and distribute an authorized generic version of Auryxia in the U.S.

Following LoE, since March 2025, our AG Partner has been selling an authorized generic version of Auryxia in the U.S.

The impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

In addition, we believe the dynamics of Auryxia reimbursement being included in the ESRD bundle and Auryxia LoE could result in the buying pattern of certain customers in future years being different than their historical practices.

License, Collaboration and Other Revenue

5 unchanged sentences

and Japan product sales recognized during the period.

Cost of product and other revenue also includes costs to manufacture drug product provided to MTPC and Medice for commercial sales of Vafseo in Japan and in the EEA, the UK, Switzerland and Australia, or collectively the Medice Territory , respectively, as well as to our AG Partner.

In addition, cost of product and other revenue includes personnel-related costs, including salaries and bonuses, employee benefits and stock-based compensation attributable to employees in particular functions and associated directly with the manufacturing of our commercial products.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 30

Cost of product and other revenue for a newly launched product does not include the full cost of manufacturing until the initial pre-launch inventory is depleted and additional inventory is manufactured and sold.

12 unchanged sentences

• costs associated with the pre-launch inventory build for Vafseo in the U.S.

prior to the FDA approval in March 2024 and in Europe prior to the European Commission, or EC , approval in April 2023.

prior to the FDA approval in March 2024.

R&D costs are expensed as incurred.

3 unchanged sentences

We cannot determine with certainty the duration and completion costs of our R&D projects, the costs of related clinical development, or if, when, or to what extent we will generate revenue from the commercialization or sale of any of our product candidates.

From inception through March 31, 2025, we have incurred $1.7 billion in R&D expenses.

From inception through June 30, 2025, we have incurred $1.7 billion in R&D expenses.

We expect to incur significant R&D expenditures for the foreseeable future as we continue the development of Auryxia, Vafseo and any other product or product candidate, including those that may be in-licensed or acquired.

5 unchanged sentences

Selling, General and Administrative Expenses

Selling, general and administrative, or SG&A , expenses consist primarily of compensation for personnel, including stock-based compensation related to commercial, marketing, executive, finance and accounting, information technology, corporate and business development and human resource functions.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 31

consulting fees), insurance costs, general corporate expenses and allocated facilities-related expenses, including rent and maintenance of facilities.

business development and human resource functions.

Other SG&A expenses include costs for marketing initiatives for our commercial products, market research and analysis on our commercial products and potential product candidates, conferences and trade shows, travel expenses, professional services fees (including legal, patent, accounting, audit, tax, and consulting fees), insurance costs, general corporate expenses and allocated facilities-related expenses, including rent and maintenance of facilities.

License Expenses

License expenses relates to royalties due to Panion & BF Biotech, Inc., or Panion , for sales of Auryxia in the U.S.

License expenses relate to royalties due to Panion & BF Biotech, Inc., or Panion , for sales of Auryxia in the U.S.

and Riona in Japan.

21 unchanged sentences

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

On February 3, 2025, we received $9.3 million on the Extended Tranche C Loan, after deducting debt issuance costs, interest, fees and expenses.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 32

Holder , we issued a warrant to the Warrant Holder to purchase 1,153,846 shares of our common stock, at an exercise price per share of $1.30.

On February 3, 2025, we received $9.3 million on the Extended Tranche C Loan, after deducting debt issuance costs, interest, fees and expenses.

On February 3, 2025, in connection with the drawdown of the Extended Tranche C Loan, in accordance with the warrant agreement, dated as of January 29, 2024, between the Company and Kreos Capital VII Aggregator SCSp, or the Warrant Holder , we issued a warrant to the Warrant Holder to purchase 1,153,846 shares of our common stock, at an exercise price per share of $1.30.

The warrant shall be exercisable for eight years from the date of issuance.

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

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

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

See Note 17, Subsequent Events , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

At-the-Market (ATM) Offering

1 unchanged sentence

Since September 12, 2024 (the date our shelf registration statement on Form S-3 went effective) through December 31, 2024, we sold 14,271,631 shares of our 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, we sold 9,437,364 shares of our common stock under this program with gross proceeds of $18.7 million ($18.4 million, net of offering expenses).

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

Akebia Therapeutics, Inc.

| Form 10-Q | Page 33

Results of Operations

Comparison of the Three Months Ended March 31, 2025 and 2024

Three Months Ended March 31,

Comparison of the Three Months Ended June 30, 2025 and 2024

Three Months Ended June 30, Change

(dollars in thousands) 2025 2024 $ %

10 unchanged sentences

License 896 762 134 18 %

Restructuring — 58 (58) *

Total operating expenses 38,464 35,326 3,138 9 %

2 unchanged sentences

Change in fair value of warrant liability (6,980) 2,331 (9,311) (399) %

Net income (loss) $ 247 $ (8,582) $ 8,829 (103) %

Product Revenue, Net— Net product revenue is derived from sales of Auryxia and Vafseo in the U.S.

We distribute Auryxia and Vafseo principally through a limited number of dialysis organizations, wholesale distributors, certain specialty pharmacy providers and our AG Partner.

Net product revenue was $60.5 million for the three months ended June 30, 2025, compared to $41.2 million for the three months ended June 30, 2024.

The increase was primarily due to Vafseo's entry to the market in January 2025 and an increase in sales volumes of Auryxia.

Auryxia lost exclusivity in the U.S.

in March 2025, which may have a negative impact on future Auryxia revenue.

We believe the dynamics of Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE scenarios.

Additionally, since March 2025, our AG Partner has been selling an authorized generic version of Auryxia in the U.S., which may slightly offset a revenue decline following the LoE.

However, our ability to continue to generate revenue from sales of Auryxia following LoE will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics that enter the market and the pricing of generics and other products on the market that compete with Auryxia.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 34

The following table summarizes our product revenue by product for the three months ended June 30, 2025 and 2024 (in thousands):

Three Months Ended June 30,

47,183 41,209

Total product revenues

$ 60,461 $ 41,209

(1) Vafseo entered the U.S.

market in January 2025.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the three months ended June 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $2.0 million for the three months ended June 30, 2025, compared to $2.4 million for the three months ended June 30, 2024.

The decrease was primarily due to revenue recognized in connection with our supply agreement with MTPC during the three months ended June 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $9.9 million for the three months ended June 30, 2025 compared to $8.0 million for the three months ended June 30, 2024.

The increase was primarily due to a $4.9 million benefit that we recorded during the three months ended June 30, 2024 due to our ability to sell inventory previously written-down as excess inventory and lower Auryxia volume during the three months ended June 30, 2024, which was partially offset by a charge of $2.1 million related to our firm purchase commitment liability during the three months ended June 30, 2024.

We began capitalizing our Vafseo costs in March 2024, in connection with the FDA's approval of Vafseo for the treatment of anemia due to CKD in adult patients on dialysis for at least three months.

Prior to the capitalization of Vafseo inventory costs, such costs were recorded as research and development expenses in the period incurred.

Cost of product and other revenue for Vafseo was $0.5 million for the three months ended June 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the three months ended June 30, 2025 was valued at cost, our cost of product and other revenue would have been $1.1 million.

As of June 30, 2025, we had $26.5 million of reduced-cost Vafseo inventory.

We expect our cost of product and other revenue for Vafseo will increase, reflecting the full cost of manufacturing, subsequent to the utilization of our reduced-cost Vafseo inventory.

Cost of Goods Sold—Amortization of Intangible Asset— Amortization of intangible asset related to the acquired developed product rights for Auryxia, and was amortized using a straight-line method over its estimated useful life of approximately six years.

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

We recorded no amortization expense and $9.0 million in amortization expense for the three months ended June 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $11.0 million for the three months ended June 30, 2025, compared to $7.6 million for the three months ended June 30, 2024.

The increase was primarily driven by increased clinical trial activities related to Vafseo as well as our other programs and higher headcount related costs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the three months ended June 30, 2025 and 2024 (in thousands):

Three Months Ended June 30,

Vafseo clinical trial and other external costs $ 4,730 $ 1,565

External costs for other programs, including feasibility and new processes and methods associated with commercial product 1,129 1,262

Total external R&D expenses 5,859 2,827

Internal personnel, consulting, facilities and other 5,154 4,820

Total R&D expenses $ 11,013 $ 7,647

Akebia Therapeutics, Inc.

| Form 10-Q | Page 35

We expect to incur significant R&D expenses in future periods in support of ongoing or planned studies with respect to the development of our product candidates as well as Vafseo.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $26.6 million for the three months ended June 30, 2025, compared to $26.9 million for the three months ended June 30, 2024.

The decrease was largely due to lower costs associated with our patient assistance program related to Auryxia and decreased professional fees, partially offset by marketing costs in connection with the Vafseo U.S.

launch during the three months ended June 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $0.9 million and $0.8 million for the three months ended June 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $6.9 million for the three months ended June 30, 2025, compared to $2.2 million for the three months ended June 30, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Termination and Settlement Agreement entered into on July 10, 2024 between us and CSL Vifor, or the Vifor Termination Agreement , partially offset by interest income related to our money market funds.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information on our arrangements with CSL Vifor.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $7.0 million and $2.3 million for the three months ended June 30, 2025 and 2024, respectively.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 36

Comparison of the Six Months Ended June 30, 2025 and 2024

Six Months Ended June 30, Change

(dollars in thousands) 2025 2024 $ %

Product revenue, net $ 116,252 $ 72,218 $ 44,034 61 %

License, collaboration and other revenue 3,556 4,037 (481) (12) %

Total revenues 119,808 76,255 43,553 57 %

Cost of goods sold

Cost of product and other revenue 17,544 10,630 6,914 65 %

Amortization of intangible asset — 18,021 (18,021) (100) %

Total cost of goods sold 17,544 28,651 (11,107) (39) %

Operating expenses

Research and development 20,767 17,379 3,388 19 %

Selling, general and administrative 52,297 52,354 (57) *

License 1,597 1,473 124 8 %

Restructuring — 58 (58) (100) %

Total operating expenses 74,661 71,264 3,397 5 %

Operating income (loss) 27,603 (23,660) 51,263 (217) %

Other expense, net (14,419) (4,591) (9,828) 214 %

Change in fair value of warrant liability (6,825) 2,201 (9,026) (410) %

Loss on extinguishment of debt — (517) 517 (100) %

3 unchanged sentences

We distribute Auryxia and Vafseo principally through a limited number of dialysis organizations, wholesale distributors, certain specialty pharmacy providers and our AG Partner.

Net product revenue was $55.8 million for the three months ended March 31, 2025, compared to $31.0 million for the three months ended March 31, 2024.

Net product revenue was $116.3 million for the six months ended June 30, 2025, compared to $72.2 million for the six months ended June 30, 2024.

The increase was primarily due to Vafseo's entry to the market in January 2025 and an increase in sales volumes of Auryxia.

2 unchanged sentences

We believe the dynamics of Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE scenarios.

Additionally, in March 2025, our AG Partner began to sell and distribute an authorized generic version of Auryxia in the U.S., which may slightly offset a revenue decline following the LoE.

However, our ability to

Additionally, since March 2025, our AG Partner has been selling an authorized generic version of Auryxia in the U.S., which may slightly offset a revenue decline following the LoE.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 37

continue to generate revenue from sales of Auryxia following LoE will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics that enter the market and the pricing of generics and other products on the market that compete with Auryxia.

The following table summarizes our product revenue by product for the three months ended March 31, 2025 and 2024 (in thousands):

Three Months Ended March 31,

The following table summarizes our product revenue by product for the six months ended June 30, 2025 and 2024 (in thousands):

Six Months Ended June 30,

90,939 72,218

3 unchanged sentences

market in January 2025.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the three months ended March 31, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $1.5 million for the three months ended March 31, 2025, compared to $1.6 million for the three months ended March 31, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $7.6 million for the three months ended March 31, 2025 compared to $2.6 million for the three months ended March 31, 2024.

The increase was primarily due to a $3.7 million benefit that we recorded during the three months ended March 31, 2024 due to our ability to sell inventory previously written-down as excess inventory and lower Auryxia volume during the three months ended March 31, 2024.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the six months ended June 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $3.6 million for the six months ended June 30, 2025, compared to $4.0 million for the six months ended June 30, 2024.

The decrease was primarily due to revenue recognized in connection with our supply agreement with MTPC during the six months ended June 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $17.5 million for the six months ended June 30, 2025 compared to $10.6 million for the six months ended June 30, 2024.

The increase was primarily due to a $8.6 million benefit that we recorded during the six months ended June 30, 2024 due to our ability to sell inventory previously written-down as excess inventory and lower Auryxia volume during the six months ended June 30, 2024, which was partially offset by a charge of $2.1 million related to our firm purchase commitment liability during the six months ended June 30, 2024.

We began capitalizing our Vafseo costs in March 2024, in connection with the FDA's approval of Vafseo for the treatment of anemia due to CKD in adult patients on dialysis for at least three months.

Prior to the capitalization of Vafseo inventory costs, such costs were recorded as research and development expenses in the period incurred.

Cost of product and other revenue for Vafseo was $1.4 million for the three months ended March 31, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the three months ended March 31, 2025 was valued at cost, our cost of product and other revenue would have been $1.9 million.

As of March 31, 2025, we had $27.6 million of reduced-cost Vafseo inventory.

Cost of product and other revenue for Vafseo was $1.9 million for the six months ended June 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the six months ended June 30, 2025 was valued at cost, our cost of product and other revenue would have been $3.0 million.

As of June 30, 2025, we had $26.5 million of reduced-cost Vafseo inventory.

We expect our cost of product and other revenue for Vafseo will increase, reflecting the full cost of manufacturing, subsequent to the utilization of our reduced-cost Vafseo inventory.

1 unchanged sentence

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

We recorded no amortization expense and $9.0 million in amortization expense for the three months ended March 31, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $9.8 million for the three months ended March 31, 2025, compared to $9.7 million for the three months ended March 31, 2024.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the three months ended March 31, 2025 and 2024 (in thousands):

Three Months Ended March 31,

We recorded no amortization expense and $18.0 million in amortization expense for the six months ended June 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $20.8 million for the six months ended June 30, 2025, compared to $17.4 million for the six months ended June 30, 2024.

The increase was primarily due to clinical trial activities related to Vafseo as well as our other programs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the six months ended June 30, 2025 and 2024 (in thousands):

Six Months Ended June 30,

Vafseo clinical trial and other external costs $ 7,760 $ 3,291

6 unchanged sentences

We expect to incur significant R&D expenses in future periods in support of ongoing or planned studies with respect to the development of our product candidates as well as Vafseo.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $25.7 million for the three months ended March 31, 2025, compared to $25.4 million for the three months ended March 31, 2024.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $0.7 million for each of the three months ended March 31, 2025 and 2024.

Restructuring Expenses— There were no restructuring expenses and $0.1 million of restructuring expenses for the three months ended March 31, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $7.6 million for the three months ended March 31, 2025, compared to $2.4 million for the three months ended March 31, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Vifor Termination Agreement.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $0.2 million and $0.1 million for the three months ended March 31, 2025 and 2024, respectively.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $52.3 million for the six months ended June 30, 2025, compared to $52.4 million for the six months ended June 30, 2024.

launch during the six months ended June 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $1.6 million and $1.5 million for the six months ended June 30, 2025 and 2024, respectively.

Restructuring Expenses— There were no restructuring expenses and $0.1 million of restructuring expenses for the six months ended June 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $14.4 million for the six months ended June 30, 2025, compared to $4.6 million for the six months ended June 30, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Vifor Termination Agreement, partially offset by interest income related to our money market funds.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $6.8 million and $2.2 million for the six months ended June 30, 2025 and 2024, respectively.

Loss on Extinguishment of Debt.

During the three months ended March 31, 2024, we recorded $0.5 million loss on the extinguishment of debt in connection with the repayment of the Pharmakon Term Loans.

We did not record any loss on the extinguishment of debt during the three months ended March 31, 2025.

During the six months ended June 30, 2024, we recorded a $0.5 million loss on the extinguishment of debt in connection with the repayment of the Pharmakon Term Loans.

We did not record any loss on the extinguishment of debt during the six months ended June 30, 2025.

Liquidity and Capital Resources

As of March 31, 2025, we had cash and cash equivalents of $113.4 million and restricted cash of $1.7 million.

As of June 30, 2025, we had cash and cash equivalents of $137.3 million and restricted cash of $1.7 million.

To date, we have funded our operations principally through sales of our common stock, including through our employee stock purchase plan, product sales, payments received from our collaboration and licensing partners, borrowings under term loans, a working capital payment from CSL Vifor also referred to as a Working Capital Fund liability and a royalty transaction.

From inception through March 31, 2025, we raised approximately $929.2 million of net proceeds from the sale of equity, including $567.9 million from various underwritten public offerings, $291.3 million from at-the-market offerings pursuant to our sales agreement with Jefferies LLC and prior sales agreements with Cantor Fitzgerald & Co., and $70.0 million from the sale of 7,571,429 shares of common stock to CSL Vifor.

We generated net operating income of $6.1 million and incurred net operating loss of $18.0 million during the three months ended March 31, 2025 and 2024, respectively.

As of March 31, 2025 and December 31, 2024, we had an accumulated deficit of $1.7 billion.

From inception through June 30, 2025, we raised approximately $929.2 million of net proceeds from the sale of equity, including $567.9 million from various underwritten public offerings, $291.3 million from at-the-market offerings pursuant to our sales agreement with Jefferies LLC and prior sales agreements with Cantor Fitzgerald & Co., and $70.0 million from the sale of 7,571,429 shares of common stock to CSL Vifor.

We generated net income of $0.2 million and $6.4 million during the three and six months ended June 30, 2025, respectively, and incurred net loss of $8.6 million and $26.6 million during the three and six months ended June 30, 2024, respectively.

As of June 30, 2025 and December 31, 2024, we had an accumulated deficit of $1.7 billion.

We had exclusive rights under a series of patents and patent applications to commercialize Auryxia in the U.S.

1 unchanged sentence

While we believe the dynamics of Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE scenarios, the impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

Additionally, in March 2025, our AG Partner began to sell and distribute an authorized generic version of Auryxia in the U.S., which may slightly offset the revenue decline following the LoE.

Additionally, since March 2025, our AG Partner has been selling an authorized generic version of Auryxia in the U.S., which may slightly offset the revenue decline following the LoE.

We believe our existing cash resources and the cash we expect to generate from product, royalty, supply and license revenues are sufficient to fund our current operating plan for the foreseeable future, including to commercialize Vafseo and Auryxia, pursue label expansion for Vafseo, and advance our other existing programs.

5 unchanged sentences

Additional financing may not be available to us in amounts or on terms acceptable to us, if at all.

If we are unable to raise additional capital in sufficient amounts when needed or on attractive terms, we may not be able to pursue development and commercial activities related to Auryxia and Vafseo, or any additional products and product candidates, including those that may be in-licensed or acquired.

Any of these events could significantly harm our business, financial condition and prospects.

There can be no assurance that the current operating plan will be achieved in the time frame anticipated by us, or that our cash resources will fund our operating plan for the period of time anticipated by us, or that additional funding will be available

Akebia Therapeutics, Inc.

| Form 10-Q | Page 39

on terms acceptable to us, or at all.

any additional products and product candidates, including those that may be in-licensed or acquired.

Any of these events could significantly harm our business, financial condition and prospects.

Our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement and involves numerous risks and uncertainties, and actual results could vary as a result of a number of factors, many of which are outside our control.

18 unchanged sentences

If we prepay the Term Loans prior to the BlackRock Maturity Date, we will be required to pay a prepayment fee ranging from 1.0% to 4.0% of the amount prepaid.

On the Closing Date, Kreos Capital VII Aggregator SCSp, an affiliate of Kreos, or the Warrant Holder , received a warrant to purchase 3,076,923 shares of our common stock, at an exercise price per share of $1.30, and upon the borrowing of Tranche C in February 2025, we issued additional warrants to purchase 1,153,846 shares of our common stock at an exercise price per share of $1.30.

On the Closing Date, the Warrant Holder received a warrant to purchase 3,076,923 shares of our common stock, at an exercise price per share of $1.30, and upon the borrowing of Tranche C in February 2025, we issued additional warrants to purchase 1,153,846 shares of our common stock at an exercise price per share of $1.30.

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

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

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

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

See Note 17, Subsequent Events , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

Liability Related to Settlement Royalties

Pursuant to the terms of the Vifor Termination Agreement, we will pay CSL Vifor decreasing quarterly tiered royalty payments ranging from a high single-digit percentage of our net sales of Vafseo up to $450.0 million to mid-single digit percentage of our net sales of Vafseo above $450.0 million, in each case, in the U.S.

On July 10, 2024, we and CSL Vifor entered into the Vifor Termination Agreement.

Pursuant to the terms of the Vifor Termination Agreement, we will pay CSL Vifor decreasing quarterly tiered royalty payments ranging from a high single-digit percentage of our net sales of Vafseo up to $450.0 million to a mid-single digit percentage of our net sales of Vafseo above $450.0 million, in each case, in the U.S.

during a calendar year, or the Settlement Royalty Payments .

The Settlement Royalty Payments commenced upon the first sale of Vafseo by us, our affiliates or third-party licensees to a third party for use in the U.S., and will continue until the later of the (i) expiration of the last-to-expire valid claim listed in the FDA OB that would be infringed by the making, using, selling or importing of Vafseo in the U.S.

The Settlement Royalty

Akebia Therapeutics, Inc.

| Form 10-Q | Page 40

Payments commenced upon the first sale of Vafseo by us, our affiliates or third-party licensees to a third party for use in the U.S., and will continue until the later of the (i) expiration of the last-to-expire valid claim listed in the FDA Orange Book that would be infringed by the making, using, selling or importing of Vafseo in the U.S.

or (ii) the expiration of marketing or regulatory exclusivity for Vafseo in the U.S., or the Settlement Royalty Term .

2 unchanged sentences

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

Akebia Therapeutics, Inc.

| Form 10-Q | Page 35

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.

2 unchanged sentences

The liability related to settlement royalties and the amortization are based on our current estimates of future royalties expected to be paid over the life of the arrangement.

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.

As of March 31, 2025, $10.6 million and $47.4 million of the settlement royalties liability is classified as a current and non-current liability, respectively.

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.

As of June 30, 2025, $14.7 million and $48.7 million of the settlement royalties liability is classified as a current and non-current liability, respectively.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

2 unchanged sentences

Pursuant to the terms of the Vifor Termination Agreement, and generally consistent with the terms of the Vifor License Agreement, we agreed to repay the Working Capital Fund to CSL Vifor through quarterly tiered royalty payments ranging from 8% to 14% of our 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 certain minimum true-up milestones.

The Working Capital Fund is considered a debt arrangement with zero coupon interest and we impute interest on the Working Capital Fund liability at a rate of 15.0% per annum.

As of March 31, 2025, $6.0 million and $34.4 million of the Working Capital Fund liability is classified as a current and non-current liability, respectively, based on management’s estimated timing of the repayment of the Working Capital Fund liability to CSL Vifor.

As of June 30, 2025, $10.0 million and $30.6 million of the Working Capital Fund liability is classified as a current and non-current liability, respectively, based on management’s estimated timing of the repayment of the Working Capital Fund liability to CSL Vifor.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

Liability Related to Sale of Future Royalties

In February 2021, we sold to HealthCare Royalty Partners IV L.P., or HCR , our right to receive royalties and sales milestones for Vafseo in Japan and certain other Asian countries, such countries collectively, the MTPC Territory , such payments collectively the Royalty Interest Payments , in each case, payable to us under the MTPC Agreement.

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

2 unchanged sentences

We amortize the liability related to the sale of future royalties using the effective interest method over the life of the arrangement.

The annual effective interest rate as of March 31, 2025 was 0%.

We retain the right to receive all potential future regulatory milestones for Vafseo under the MTPC Agreement.

We recorded $0.4 million of non-cash royalty revenue during each of the three months ended March 31, 2025 and 2024.

As of March 31, 2025, $2.0 million and $51.5 million of the liability related to the sale of future royalties is classified as a current and non-current liability, respectively.

The annual effective interest rate as of June 30, 2025 was 0%.

We retain the right to receive all potential future

Akebia Therapeutics, Inc.

| Form 10-Q | Page 41

regulatory milestones for Vafseo under the MTPC Agreement.

We recorded non-cash royalty revenue of $0.5 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, $2.2 million and $51.1 million of the liability related to the sale of future royalties is classified as a current and non-current liability, respectively.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

1 unchanged sentence

Letter of Credit

Akebia Therapeutics, Inc.

| Form 10-Q | Page 36

As of March 31, 2025, in connection with the Cambridge Lease (as defined below), we had $1.7 million in a letter of credit outstanding.

As of June 30, 2025, in connection with the Cambridge Lease (as defined below), we had $1.7 million in a letter of credit outstanding.

Director and Officer Indemnification

3 unchanged sentences

We are party to contractual obligations involving commitments to make payments to third parties in the future.

Certain contractual obligations are reflected on our condensed consolidated balance sheet as of March 31, 2025, while others are considered future obligations.

Our material cash requirements as of March 31, 2025, include contractual obligations and commitments arising in the normal course of business, including leases, license agreements, manufacturing agreements and unconditional purchase commitments which are described in more detail below.

Certain contractual obligations are reflected on our condensed consolidated balance sheet as of June 30, 2025, while others are considered future obligations.

Our material cash requirements as of June 30, 2025, include contractual obligations and commitments arising in the normal course of business, including leases, license agreements, manufacturing agreements and unconditional purchase commitments which are described in more detail below.

Cambridge Lease

8 unchanged sentences

Cyclerion Agreement

In June 2021, we entered into the Cyclerion Agreement with Cyclerion, as amended in December 2024, under which we 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, we entered into a license agreement, or the Cyclerion Agreement , with Cyclerion, as amended in December 2024, under which we 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 Cyclerion Agreement, as amended, Cyclerion is eligible to receive up to an aggregate of $198.5 million from us in specified development and regulatory milestone payments on a product-by-product basis.

3 unchanged sentences

We have various supply arrangements to which we are a party, and we are obligated to pay for drug substance and drug product for commercial use.

Under one of our agreements, we are required to purchase a minimum quantity of Auryxia drug substance at a predetermined price.

Under one of our agreements, we are required to purchase a minimum quantity of Auryxia drug

Akebia Therapeutics, Inc.

| Form 10-Q | Page 42

substance at a predetermined price.

We are also obligated to purchase a certain percentage of the global demand for Vafseo drug substance and drug product based on certain quarterly and annual forecasts we provide to certain suppliers.

4 unchanged sentences

On December 22, 2022, we and BioVectra terminated any and all existing agreements for BioVectra to supply us Auryxia drug substance.

Under the BioVectra Termination Agreement, we agreed to pay BioVectra a total of $32.5 million consisting of (i)

Akebia Therapeutics, Inc.

| Form 10-Q | Page 37

an upfront payment of $17.5 million that was paid in December 2022 and (ii) six quarterly payments of $2.5 million which commenced in April 2024.

Under the BioVectra Termination Agreement, we agreed to pay BioVectra a total of $32.5 million consisting of (i) an upfront payment of $17.5 million that was paid in December 2022 and (ii) six quarterly payments of $2.5 million which commenced in April 2024 and were completed in July 2025.

In addition, we and BioVectra have released one another from all existing and future claims and liabilities and agreed to return certain materials and documents.

4 unchanged sentences

Payments due upon cancellation consist only of payments for services provided or expenses incurred, including non-cancellable obligations of service providers, up to the date of cancellation.

In addition, we contract with various organizations to conduct R&D activities with remaining contract costs to us of approximately $42.2 million as of March 31, 2025.

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

In addition, we contract with various organizations to conduct R&D activities with remaining contract costs to us of approximately $57.7 million as of 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 us upon written notice.

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

The following table provides a summary of cash flow data for each applicable period:

Three Months Ended March 31,

Six Months Ended June 30,

NET CASH PROVIDED BY/(USED IN) ( in thousands ):

2 unchanged sentences

Financing activities 76,662 26,115

Decrease in cash, cash equivalents and restricted cash $ 61,509 $ (957)

Increase (decrease) in cash, cash equivalents and restricted cash $ 85,448 $ (3,412)

Cash, cash equivalents and restricted cash — beginning of period 53,550 44,579

1 unchanged sentence

Operating Activities

Net cash used in operating activities was $13.6 million for the three months ended March 31, 2025.

Net cash used in operating activities for the three months ended March 31, 2025 consisted of a net income of $6.1 million reduced by net non-cash adjustments of $10.0 million, including a change in fair value of the warrant liability of $0.2 million, offset by a reduction of $29.7 million in working capital.

Net cash used in operating activities was $19.4 million for the three months ended March 31, 2024.

Net cash provided by operating activities was $8.8 million for the six months ended June 30, 2025.

Net cash provided by operating activities for the six months ended June 30, 2025 consisted of net income of $6.4 million as well as net non-cash adjustments of $27.0 million, including a change in fair value of the warrant liability of $6.8 million, offset by a reduction of $24.6 million in working capital.

Net cash used in operating activities was $29.5 million for the six months ended June 30, 2024.

Net cash used in operating activities consisted of a net loss of $26.6 million and net non-cash adjustments of $25.9 million, including amortization of our intangible asset of $18.0 million, and a reduction of $28.8 million in working capital.

Investing Activities

Net cash provided by investing activities for the three months ended March 31, 2025 of $0.2 million primarily consisted of proceeds from the sale of property and equipment.

No net cash was used in investing activities for the three months ended March 31, 2024.

Immaterial net cash was provided by investing activities for the six months ended June 30, 2025.

Immaterial net cash was used in investing activities for the six months ended June 30, 2024.

Financing Activities

Net cash provided by financing activities was $74.9 million for the three months ended March 31, 2025, which primarily consisted of proceeds of $10.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $64.9 million from the sale of common stock from our March 2025 underwritten public offering and under our ATM facility.

Net cash provided by financing activities was $18.5 million for the three months ended March 31, 2024, which primarily consisted of proceeds of $37.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $18.7 million from the sale of common stock under our ATM Facility partially offset by principal payments of debt of $36.7 million primarily related to the Pharmakon Term Loans which were repaid in January 2024.

Recent Accounting Pronouncements

For a discussion of recent accounting pronouncements, see Note 2, Summary of Significant Accounting Policies , of the Notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Quarterly Report on Form 10-Q.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 43

Net cash provided by financing activities was $76.7 million for the six months ended June 30, 2025, which primarily consisted of proceeds of $10.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $66.4 million from the sale of common stock from our March 2025 underwritten public offering and under our ATM facility.

Net cash provided by financing activities was $26.1 million for the six months ended June 30, 2024, which primarily consisted of proceeds of $45.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $18.7 million from the sale of common stock under our ATM Facility, partially offset by principal payments of debt of $37.1 million primarily related to the Pharmakon Term Loans which were repaid in January 2024.

Recent Accounting Pronouncements

Critical Accounting Estimates and Significant Judgments

6 unchanged sentences

In making estimates and judgments, management employs critical accounting policies.

During the three months ended March 31, 2025, there were no material changes to our methodologies used for our critical accounting estimates as reported in our 2024 Form 10-K.

During the six months ended June 30, 2025, there were no material changes to our methodologies used for our critical accounting estimates as reported in our 2024 Form 10-K.

Quantitative and Qualitative Disclosures about Market Risk.

1 unchanged sentence

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 2. Management’s Discussion and Analysis