| 1. Round | 08/08/2016 | VfB Stuttgart | - | FC St. Pauli | 2:1 | ||||
| 2. Round | 13/08/2016 | FC St. Pauli | - | Eintracht Braunschweig | 0:2 | ||||
| 3. Round | 28/08/2016 | Dynamo Dresden | - | FC St. Pauli | 1:0 | ||||
| 10. Round | 22/10/2016 | SV Sandhausen | - | FC St. Pauli | 3:0 | ||||
| 12. Round | 07/11/2016 | Würzburger Kickers | - | FC St. Pauli | 1:0 | ||||
| 16. Round | 11/12/2016 | SpVgg Greuther Fürth | - | FC St. Pauli | 0:2 |
USA
