| 18. Round | 29/01/2017 | FC St. Pauli | - | VfB Stuttgart | 0:1 | ||||
| 19. Round | 05/02/2017 | Eintracht Braunschweig | - | FC St. Pauli | 1:2 | ||||
| 20. Round | 12/02/2017 | FC St. Pauli | - | Dynamo Dresden | 2:0 | ||||
| 22. Round | 27/02/2017 | FC St. Pauli | - | Karlsruher SC | 5:0 | ||||
| 23. Round | 04/03/2017 | TSV 1860 München | - | FC St. Pauli | 1:2 | ||||
| 24. Round | 10/03/2017 | FC St. Pauli | - | 1. FC Union Berlin | 1:2 | ||||
| 25. Round | 18/03/2017 | FC St. Pauli | - | Hannover 96 | 0:0 | ||||
| 26. Round | 31/03/2017 | Erzgebirge Aue | - | FC St. Pauli | 1:0 | ||||
| 27. Round | 04/04/2017 | FC St. Pauli | - | SV Sandhausen | 0:0 | ||||
| 29. Round | 16/04/2017 | FC St. Pauli | - | Würzburger Kickers | 1:0 | ||||
| 30. Round | 21/04/2017 | Fortuna Düsseldorf | - | FC St. Pauli | 1:3 | ||||
| 31. Round | 28/04/2017 | FC St. Pauli | - | 1. FC Heidenheim 1846 | 3:0 |  |
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| 32. Round | 05/05/2017 | 1. FC Kaiserslautern | - | FC St. Pauli | 1:2 | ||||
| 33. Round | 14/05/2017 | FC St. Pauli | - | SpVgg Greuther Fürth | 1:1 | ||||
| 34. Round | 21/05/2017 | VfL Bochum | - | FC St. Pauli | 1:3 |  |
Germany