| 1. Round | 30/07/2016 | VfL Wolfsburg II | - | ETSV Weiche Flensburg | 2:2 | ||||
| 2. Round | 06/08/2016 | SV Meppen | - | ETSV Weiche Flensburg | 3:0 | ||||
| 4. Round | 10/08/2016 | Eintracht Norderstedt | - | ETSV Weiche Flensburg | 1:2 | ||||
| 3. Round | 14/08/2016 | ETSV Weiche Flensburg | - | Lüneburger SK Hansa | 0:1 | ||||
| 5. Round | 28/08/2016 | ETSV Weiche Flensburg | - | VfB Oldenburg | 3:1 | ||||
| 15. Round | 05/11/2016 | FC St. Pauli II | - | ETSV Weiche Flensburg | 0:0 | ||||
| 18. Round | 27/11/2016 | ETSV Weiche Flensburg | - | VfL Wolfsburg II | 0:0 | ||||
| 19. Round | 04/12/2016 | ETSV Weiche Flensburg | - | SV Meppen | 3:1 |  |
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| 22. Round | 19/02/2017 | VfB Oldenburg | - | ETSV Weiche Flensburg | 1:2 | ||||
| 24. Round | 05/03/2017 | SV Eichede | - | ETSV Weiche Flensburg | 1:1 | ||||
| 25. Round | 12/03/2017 | ETSV Weiche Flensburg | - | Hannover 96 II | 1:0 | ||||
| 30. Round | 23/04/2017 | ETSV Weiche Flensburg | - | VfV Hildesheim | 4:2 | ||||
| 33. Round | 13/05/2017 | VfB Lübeck | - | ETSV Weiche Flensburg | 2:0 |
Germany