| 2. Round | 20/08/2016 | Dynamo Dresden [Youth B] | - | FC St. Pauli [Youth B] | 2:2 | ||||
| 3. Round | 28/08/2016 | Holstein Kiel [Youth B] | - | FC St. Pauli [Youth B] | 2:2 | ||||
| 5. Round | 17/09/2016 | VfL Wolfsburg [Youth B] | - | FC St. Pauli [Youth B] | 3:2 | ||||
| 12. Round | 12/11/2016 | FC St. Pauli [Youth B] | - | 1. FC Magdeburg [Youth B] | 2:0 | ||||
| 15. Round | 10/12/2016 | FC St. Pauli [Youth B] | - | Dynamo Dresden [Youth B] | 0:2 | ||||
| 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 | ||||
| 21. Round | 18/03/2017 | Hansa Rostock [Youth B] | - | FC St. Pauli [Youth B] | 1:2 | ||||
| 23. Round | 09/04/2017 | TeBe Berlin [Youth B] | - | FC St. Pauli [Youth B] | 0:0 | ||||
| 25. Round | 21/05/2017 | 1. FC Magdeburg [Youth B] | - | FC St. Pauli [Youth B] | 2:1 |
Germany