| 7. Round | 08/10/2016 | Hamburger SV [Youth B] | - | FC St. Pauli [Youth B] | 2:2 | ||||
| 11. Round | 05/11/2016 | Hertha BSC [Youth B] | - | FC St. Pauli [Youth B] | 1:3 | ||||
| 14. Round | 04/12/2016 | RB Leipzig [Youth B] | - | FC St. Pauli [Youth B] | 1:2 | ||||
| 15. Round | 10/12/2016 | FC St. Pauli [Youth B] | - | Dynamo Dresden [Youth B] | 0:2 | ||||
| 16. Round | 17/12/2016 | FC St. Pauli [Youth B] | - | Holstein Kiel [Youth B] | 3:1 | ||||
| 10. Round | 12/02/2017 | FC St. Pauli [Youth B] | - | TeBe Berlin [Youth B] | 3:1 | ||||
| 17. Round | 19/02/2017 | Niendorfer TSV [Youth B] | - | FC St. Pauli [Youth B] | 0:6 | ||||
| 19. Round | 05/03/2017 | 1. FC Union Berlin [Youth B] | - | FC St. Pauli [Youth B] | 0:1 | ||||
| 22. Round | 01/04/2017 | FC St. Pauli [Youth B] | - | Eintracht Braunschweig [Youth B] | 4:0 | ||||
| 25. Round | 21/05/2017 | 1. FC Magdeburg [Youth B] | - | FC St. Pauli [Youth B] | 2:1 | ||||
| 26. Round | 28/05/2017 | FC St. Pauli [Youth B] | - | Werder Bremen [Youth B] | 1:5 |
Germany