| 1. Round | 14/08/2016 | FCE Rheine | - | SpVgg Erkenschwick | 0:4 | ||||
| 4. Round | 04/09/2016 | SV Lippstadt 08 | - | FCE Rheine | 2:1 | ||||
| 5. Round | 11/09/2016 | FCE Rheine | - | Westfalia Rhynern | 2:0 | ||||
| 6. Round | 18/09/2016 | SuS Neuenkirchen | - | FCE Rheine | 1:4 | ||||
| 8. Round | 02/10/2016 | FCE Rheine | - | FC Brünninghausen | 3:1 | ||||
| 9. Round | 09/10/2016 | FCE Rheine | - | 1. FC Kaan-Marienborn | 0:0 | ||||
| 10. Round | 16/10/2016 | SC Paderborn 07 II | - | FCE Rheine | 0:0 | ||||
| 11. Round | 23/10/2016 | FCE Rheine | - | SuS Stadtlohn | 3:1 | ||||
| 12. Round | 30/10/2016 | TuS Erndtebrück | - | FCE Rheine | 4:0 | ||||
| 13. Round | 06/11/2016 | FCE Rheine | - | Roland Beckum | 3:0 |  |
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| 14. Round | 13/11/2016 | Hammer SpVg | - | FCE Rheine | 3:2 | ||||
| 15. Round | 27/11/2016 | ASC 09 Dortmund | - | FCE Rheine | 7:1 | ||||
| 20. Round | 18/02/2017 | Arminia Bielefeld II | - | FCE Rheine | 1:1 | |
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| 19. Round | 25/02/2017 | FCE Rheine | - | FC Gütersloh 2000 | 2:0 | ||||
| 22. Round | 12/03/2017 | Westfalia Rhynern | - | FCE Rheine | 2:1 | ||||
| 23. Round | 19/03/2017 | FCE Rheine | - | SuS Neuenkirchen | 4:0 | ||||
| 24. Round | 26/03/2017 | TuS Ennepetal | - | FCE Rheine | 2:3 |
Germany