Seaport Therapeutics, Inc.

Comparison of the three months ended September 30, 2026 and 2025

The following table summarizes our results of operations (in thousands):

The following table summarizes our research and development expenses (in thousands):

Research and development expenses increased by $3.4 million from $20.5 million for the three months ended September 30, 2025 to $23.9 million for the three months ended September 30, 2026. The increase in research and development expenses was primarily attributable to:

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$2.5 million of increased costs associated with our lead program GlyphAllo, which was primarily due to the advancement of our Phase 2b BUOY-1 trial which commenced in July 2025 and other supporting clinical studies;

•

$0.9 million of increased costs associated with advancing our nonclinical and early discovery assets;

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$0.5 million of increased costs associated with employee compensation primarily due to increased headcount to support our research and development operations and salary adjustments; and

•

$0.3 million of increased costs associated with non-cash stock-based compensation primarily due to additional equity grants issued under our 2024 and 2026 Equity Plans;

These increases were partially offset by:

•

$(0.8) million of decreased costs associated with our GlyphAgo program, primarily due to a reduction in non-clinical activities, partially offset by the initiation of our Phase 2a trial; and

•

$(0.1) million of decreased costs associated with our Glyph2BLSD program due to timing of our development activities;

The following table summarizes our general and administrative expenses (in thousands):

General and administrative expenses increased by $1.5 million from $5.0 million for the three months ended September 30, 2025 to $6.5 million for the three months ended September 30, 2026. The increase in general and administrative expenses was primarily attributable to:

•

$0.3 million of increased employee compensation due to increased headcount and salary adjustments;

•

$0.3 million of increased costs associated with non-cash stock-based compensation primarily due to additional equity grants issued under our 2024 and 2026 Equity Plans;

•

$0.4 million of increased professional fees primarily due to higher audit, legal, and consulting fees as a result of operating as a public company; and

•

$0.4 million of increased facilities, depreciation, IT, and other costs primarily due to increased public company directors and officers insurance costs.

Other Income, Net

Other income, net, increased by $1.1 million from $3.0 million for the three months ended September 30, 2025 to $4.1 million for the three months ended September 30, 2026. The increase in other income, net was primarily attributed to an increase in interest income on our investments and cash equivalents due to the investment of funds received from our IPO in May 2026.

Income tax provision

Income tax provision increased $32 thousand for the three months ended September 30, 2026 compared to the three months ended September 30, 2025. The increase in the income tax provision was attributed to foreign income taxes related to our Australian subsidiary primarily as a result of our research and development tax credit and transfer pricing agreement with Seaport Therapeutics, Inc.

Comparison of the nine months ended September 30, 2026 and 2025

The following table summarizes our results of operations (in thousands):

The following table summarizes our research and development expenses (in thousands):

Research and development expenses increased by $25.5 million from $44.4 million for the nine months ended September 30, 2025 to $69.9 million for the nine months ended September 30, 2026. The increase in research and development expenses was primarily attributable to:

•

$15.5 million of increased costs associated with our lead program GlyphAllo, which was primarily due to advancement of our Phase 2b BUOY-1 trial which commenced in July 2025 and other supporting clinical studies;

•

$5.2 million of increased costs associated with our GlyphAgo program, which was primarily due to the completion of our Phase 1 trial, commencement of our Phase 2a trial, and other development activities as we advance the program;

•

$1.4 million of increased costs associated with advancing our nonclinical and early discovery assets;

•

$2.2 million of increased costs associated with employee compensation primarily due to increased headcount to support our research and development operations and salary adjustments;

•

$1.0 million of increased costs associated with non-cash stock-based compensation costs primarily due to additional equity grants issued under our 2024 and 2026 Equity Plans; and

•

$0.4 million of increased costs associated with other research and development expenses due to increased development and regulatory software costs and additional travel to support our clinical studies and manufacturing activities.

These increases were partially offset by:

•

$0.3 million of decreased costs associated with our Glyph2BLSD program due to timing of our development activities.

The following table summarizes our general and administrative expenses (in thousands):

General and administrative expenses increased by $38.1 million from $15.7 million for the nine months ended September 30, 2025 to $53.8 million for the nine months ended September 30, 2026. The increase in general and administrative expenses was primarily attributable to:

•

$35.7 million of increased costs associated with non-cash stock-based compensation costs primarily due to fully vested awards issued and awards accelerated upon the successful completion of the IPO, as described in previous SEC filings, and additional equity grants issued under our 2024 and 2026 Equity Plans;

•

$1.0 million of increased employee compensation due to increased headcount and salary adjustments;

•

$0.7 million of increased facilities, depreciation, IT, and other costs primarily due to increased public company directors and officers insurance costs; and

•

$0.6 million of increased professional fees primarily due to higher audit, consulting, and board of director fees as a result of operating as a public company.

Other Income, Net

Other income, net increased by $0.6 million from $9.6 million for the nine months ended September 30, 2025 to $10.2 million for the nine months ended September 30, 2026. The increase in other income, net was primarily attributed to an increase in interest income on our investments and cash equivalents due to the investment of funds received from our IPO in May 2026.

Income tax provision

Income tax provision increased by $0.6 million from $0.3 million for the nine months ended September 30, 2025 to $0.9 million for the nine months ended September 30, 2026. The increase in the income tax provision was attributed to foreign income taxes related to our Australian subsidiary primarily as a result of our research and development tax credit and transfer pricing agreement with Seaport Therapeutics, Inc.