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S-3 424B5 EX-FILING FEES 333-281503 0001974640 Apogee Therapeutics, Inc. N/A N/A The prospectus is not a final prospectus for the related offering. 0001974640 2025-10-09 2025-10-09 0001974640 1 2025-10-09 2025-10-09 0001974640 2 2025-10-09 2025-10-09 iso4217:USD xbrli:pure xbrli:shares

Calculation of Filing Fee Tables

S-3

Apogee Therapeutics, Inc.

Table 1: Newly Registered and Carry Forward Securities ☐Not Applicable

Security Type

Security Class Title

Fee Calculation or Carry Forward Rule

Amount Registered

Proposed Maximum Offering Price Per Unit

Maximum Aggregate Offering Price

Fee Rate

Amount of Registration Fee

Carry Forward Form Type

Carry Forward File Number

Carry Forward Initial Effective Date

Filing Fee Previously Paid in Connection with Unsold Securities to be Carried Forward

Newly Registered Securities
Fees to be Paid 1 Equity Common stock, par value $0.00001 per share 457(r) 8,414,635 $ 41.00 $ 345,000,035.00 0.0001381 $ 47,644.50
Fees to be Paid 2 Equity Pre-funded warrants to purchase common stock 457(r) 365,853 $ 40.9999 $ 0.00 0.0001381 $ 0.00
Fees Previously Paid
Carry Forward Securities
Carry Forward Securities

Total Offering Amounts:

$ 345,000,035.00

$ 47,644.50

Total Fees Previously Paid:

$ 0.00

Total Fee Offsets:

$ 0.00

Net Fee Due:

$ 47,644.50

Offering Note

1

(a) Assumes exercise in full of the underwriters' option to purchase up to 1,097,560 additional shares of common stock and includes 365,853 shares of common stock issuable upon the exercise of the pre-funded warrants to purchase common stock. (b) Represents the sum of the offering price of the pre-funded warrants of $40.99999 per pre-funded warrant and the exercise price of $0.00001 per share issuable pursuant to the pre-funded warrants. (c) The registration fee is calculated in accordance with Rule 457(r) of the Securities Act and represents deferred payment of the registration fees in connection with the Registrant's registration statement on Form S-3ASR (Registration No. 333-281503) paid with the filing of this prospectus supplement.

2

(a) Pursuant to Rule 416 under the Securities Act, the pre-funded warrants to purchase common stock being registered hereunder include such indeterminate number of additional shares of common stock as may be issued after the date hereof as a result of share splits, share dividends or similar transactions. (b) The registration fee for the pre-funded warrants is being allocated to the shares of common stock issuable upon exercise of the pre-funded warrants.
Table 2: Fee Offset Claims and Sources ☑Not Applicable
Registrant or Filer Name Form or Filing Type File Number Initial Filing Date Filing Date Fee Offset Claimed Security Type Associated with Fee Offset Claimed Security Title Associated with Fee Offset Claimed Unsold Securities Associated with Fee Offset Claimed Unsold Aggregate Offering Amount Associated with Fee Offset Claimed Fee Paid with Fee Offset Source
Rules 457(b) and 0-11(a)(2)
Fee Offset Claims N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
Fee Offset Sources N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
Rule 457(p)
Fee Offset Claims N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
Fee Offset Sources N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
Table 3: Combined Prospectuses ☑Not Applicable

Security Type

Security Class Title

Amount of Securities Previously Registered

Maximum Aggregate Offering Price of Securities Previously Registered

Form Type

File Number

Initial Effective Date

N/A N/A N/A N/A N/A N/A N/A N/A