| 1. Round | 14/08/2016 | FC Carl Zeiss Jena [Youth] | - | FC St. Pauli [Youth] | 2:2 |  |
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| 2. Round | 17/08/2016 | FC St. Pauli [Youth] | - | RB Leipzig [Youth] | 1:2 | ||||
| 4. Round | 27/08/2016 | Hertha BSC [Youth] | - | FC St. Pauli [Youth] | 6:3 | ||||
| 5. Round | 11/09/2016 | FC St. Pauli [Youth] | - | Hannover 96 [Youth] | 1:2 | ||||
| 6. Round | 16/09/2016 | Hamburger SV [Youth] | - | FC St. Pauli [Youth] | 3:1 | ||||
| 7. Round | 24/09/2016 | FC St. Pauli [Youth] | - | Holstein Kiel [Youth] | 1:2 | ||||
| 11. Round | 05/11/2016 | FC St. Pauli [Youth] | - | VfL Wolfsburg [Youth] | 0:2 | ||||
| 14. Round | 03/12/2016 | FC St. Pauli [Youth] | - | FC Carl Zeiss Jena [Youth] | 0:1 | ||||
| 15. Round | 10/12/2016 | RB Leipzig [Youth] | - | FC St. Pauli [Youth] | 7:1 | ||||
| 16. Round | 05/02/2017 | VfL Osnabrück [Youth] | - | FC St. Pauli [Youth] | 2:1 | ||||
| 17. Round | 11/02/2017 | FC St. Pauli [Youth] | - | Hertha BSC [Youth] | 2:3 | ||||
| 22. Round | 01/04/2017 | Eintracht Braunschweig [Youth] | - | FC St. Pauli [Youth] | 0:3 | |
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| 26. Round | 06/05/2017 | Werder Bremen [Youth] | - | FC St. Pauli [Youth] | 1:2 |
Germany