| 15. Round | 05/11/2016 | FC St. Pauli II | - | ETSV Weiche Flensburg | 0:0 | ||||
| 19. Round | 03/12/2016 | FC St. Pauli II | - | TSV Havelse | 0:2 | ||||
| 20. Round | 05/02/2017 | VfB Lübeck | - | FC St. Pauli II | 1:1 |  |
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| 24. Round | 05/03/2017 | Lüneburger SK Hansa | - | FC St. Pauli II | 1:1 | ||||
| 28. Round | 01/04/2017 | SV Eichede | - | FC St. Pauli II | 3:0 | ||||
| 27. Round | 04/04/2017 | FC St. Pauli II | - | Hamburger SV II | 1:3 | ||||
| 21. Round | 13/04/2017 | FC St. Pauli II | - | SV Drochtersen/Assel | 1:0 | ||||
| 26. Round | 16/04/2017 | VfB Oldenburg | - | FC St. Pauli II | 2:0 | ||||
| 30. Round | 22/04/2017 | U.S.I. Lupo-Martini | - | FC St. Pauli II | 1:2 | ||||
| 31. Round | 30/04/2017 | FC St. Pauli II | - | Eintracht Braunschweig II | 1:2 | ||||
| 32. Round | 05/05/2017 | ETSV Weiche Flensburg | - | FC St. Pauli II | 1:0 | ||||
| 33. Round | 13/05/2017 | FC St. Pauli II | - | Schwarz-Weiß Rehden | 2:2 | ||||
| 34. Round | 20/05/2017 | VfV Hildesheim | - | FC St. Pauli II | 1:1 |
Germany