| 3. Round | 19/08/2023 | SpVgg Greuther Fürth | - | FC St. Pauli | 0:0 | ||||
| 6. Round | 17/09/2023 | FC St. Pauli | - | Holstein Kiel | 5:1 | ||||
| 10. Round | 21/10/2023 | SC Paderborn 07 | - | FC St. Pauli | 2:2 |  |
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| 12. Round | 03/11/2023 | SV 07 Elversberg | - | FC St. Pauli | 0:2 | ||||
| 18. Round | 20/01/2024 | FC St. Pauli | - | 1. FC Kaiserslautern | 2:0 | ||||
| 20. Round | 03/02/2024 | FC St. Pauli | - | SpVgg Greuther Fürth | 3:2 | ||||
| 23. Round | 23/02/2024 | Holstein Kiel | - | FC St. Pauli | 3:4 | ||||
| 24. Round | 01/03/2024 | FC Schalke 04 | - | FC St. Pauli | 3:1 | ||||
| 25. Round | 10/03/2024 | FC St. Pauli | - | Hertha BSC | 2:0 | ||||
| 26. Round | 16/03/2024 | 1. FC Nürnberg | - | FC St. Pauli | 0:2 | |
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| 27. Round | 31/03/2024 | FC St. Pauli | - | SC Paderborn 07 | 2:1 | ||||
| 28. Round | 06/04/2024 | Karlsruher SC | - | FC St. Pauli | 2:1 | ||||
| 29. Round | 14/04/2024 | FC St. Pauli | - | SV 07 Elversberg | 3:4 | ||||
| 30. Round | 21/04/2024 | Hannover 96 | - | FC St. Pauli | 1:2 | ||||
| 31. Round | 26/04/2024 | FC St. Pauli | - | Hansa Rostock | 1:0 | ||||
| 33. Round | 12/05/2024 | FC St. Pauli | - | VfL Osnabrück | 3:1 | |
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| 34. Round | 19/05/2024 | SV Wehen Wiesbaden | - | FC St. Pauli | 1:2 |
Poland