| 4. Round | 26/08/2023 | FC St. Pauli [Youth] | - | Hannover 96 [Youth] | 1:1 | ||||
| 5. Round | 16/09/2023 | Hertha BSC [Youth] | - | FC St. Pauli [Youth] | 8:1 | ||||
| 6. Round | 23/09/2023 | FC St. Pauli [Youth] | - | Dynamo Dresden [Youth] | 1:2 |  |
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| 7. Round | 30/09/2023 | Eintracht Braunschweig [Youth] | - | FC St. Pauli [Youth] | 1:2 | ||||
| 8. Round | 15/10/2023 | FC St. Pauli [Youth] | - | SV Meppen [Youth] | 1:0 | ||||
| 9. Round | 29/10/2023 | 1. FC Union Berlin [Youth] | - | FC St. Pauli [Youth] | 3:1 | ||||
| 10. Round | 04/11/2023 | Werder Bremen [Youth] | - | FC St. Pauli [Youth] | 2:1 |  |
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| 14. Round | 09/12/2023 | FC St. Pauli [Youth] | - | RB Leipzig [Youth] | 1:0 | ||||
| 15. Round | 03/02/2024 | VfL Osnabrück [Youth] | - | FC St. Pauli [Youth] | 2:2 | |
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| 16. Round | 10/02/2024 | FC St. Pauli [Youth] | - | Hansa Rostock [Youth] | 2:1 | ||||
| 18. Round | 24/02/2024 | FC St. Pauli [Youth] | - | Hertha BSC [Youth] | 0:1 | ||||
| 19. Round | 02/03/2024 | Dynamo Dresden [Youth] | - | FC St. Pauli [Youth] | 1:0 | |
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| 23. Round | 20/04/2024 | FC St. Pauli [Youth] | - | Werder Bremen [Youth] | 2:3 | ||||
| 24. Round | 27/04/2024 | FC Carl Zeiss Jena [Youth] | - | FC St. Pauli [Youth] | 3:6 | |
Germany