| 1. Round | 29/07/2016 | Flensburg 08 | - | Heider SV | 3:2 | ||||
| 10. Round | 18/09/2016 | Flensburg 08 | - | Kilia Kiel | 4:2 |  |
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| 11. Round | 24/09/2016 | TSV Lägerdorf | - | Flensburg 08 | 1:0 | ||||
| 12. Round | 01/10/2016 | Flensburg 08 | - | TSB Flensburg | 1:1 | ||||
| 13. Round | 09/10/2016 | TuS Hartenholm | - | Flensburg 08 | 1:4 | ||||
| 14. Round | 15/10/2016 | Flensburg 08 | - | TSV Kropp | 6:1 | ||||
| 15. Round | 22/10/2016 | TSV Altenholz | - | Flensburg 08 | 0:6 | ||||
| 16. Round | 29/10/2016 | Flensburg 08 | - | NTSV Strand 08 | 2:0 | ||||
| 17. Round | 05/11/2016 | PSV Union Neumünster | - | Flensburg 08 | 1:4 | ||||
| 18. Round | 13/11/2016 | SV Todesfelde | - | Flensburg 08 | 2:0 | ||||
| 19. Round | 19/11/2016 | Flensburg 08 | - | Concordia Schönkirchen | 5:0 | ||||
| 20. Round | 26/11/2016 | Oldenburger SV | - | Flensburg 08 | 1:2 |  |
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| 24. Round | 12/03/2017 | VfR Neumünster | - | Flensburg 08 | 2:2 | ||||
| 26. Round | 25/03/2017 | Kilia Kiel | - | Flensburg 08 | 0:1 | ||||
| 27. Round | 01/04/2017 | Flensburg 08 | - | TSV Lägerdorf | 3:0 | ||||
| 28. Round | 08/04/2017 | TSB Flensburg | - | Flensburg 08 | 5:2 | |
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| 25. Round | 17/04/2017 | Flensburg 08 | - | TSV Schilksee | 2:2 | ||||
| 29. Round | 22/04/2017 | Flensburg 08 | - | TuS Hartenholm | 1:5 |
Germany