| 1. Round | 13/08/2016 | FC St. Pauli [Youth B] | - | RB Leipzig [Youth B] | 2:3 | ||||
| 10. Round | 12/02/2017 | FC St. Pauli [Youth B] | - | TeBe Berlin [Youth B] | 3:1 |  |
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| 17. Round | 19/02/2017 | Niendorfer TSV [Youth B] | - | FC St. Pauli [Youth B] | 0:6 | |
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| 18. Round | 26/02/2017 | FC St. Pauli [Youth B] | - | VfL Wolfsburg [Youth B] | 3:0 | ||||
| 19. Round | 05/03/2017 | 1. FC Union Berlin [Youth B] | - | FC St. Pauli [Youth B] | 0:1 | ||||
| 20. Round | 12/03/2017 | FC St. Pauli [Youth B] | - | Hamburger SV [Youth B] | 0:2 | ||||
| 21. Round | 18/03/2017 | Hansa Rostock [Youth B] | - | FC St. Pauli [Youth B] | 1:2 | ||||
| 22. Round | 01/04/2017 | FC St. Pauli [Youth B] | - | Eintracht Braunschweig [Youth B] | 4:0 | ||||
| 23. Round | 09/04/2017 | TeBe Berlin [Youth B] | - | FC St. Pauli [Youth B] | 0:0 | ||||
| 24. Round | 22/04/2017 | FC St. Pauli [Youth B] | - | Hertha BSC [Youth B] | 0:0 | ||||
| 26. Round | 28/05/2017 | FC St. Pauli [Youth B] | - | Werder Bremen [Youth B] | 1:5 |
Germany