| 1. Round | 14/08/2016 | Hammer SpVg | - | FC Gütersloh 2000 | 4:1 |  |
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| 2. Round | 21/08/2016 | FC Gütersloh 2000 | - | FCE Rheine | 0:2 | ||||
| 4. Round | 04/09/2016 | FC Gütersloh 2000 | - | SC Hassel | 2:0 | ||||
| 6. Round | 18/09/2016 | FC Gütersloh 2000 | - | ASC 09 Dortmund | 4:2 | |
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| 7. Round | 25/09/2016 | FC Gütersloh 2000 | - | Arminia Bielefeld II | 4:2 | ||||
| 21. Round | 05/03/2017 | SC Hassel | - | FC Gütersloh 2000 | 1:3 | ||||
| 22. Round | 12/03/2017 | FC Gütersloh 2000 | - | SpVgg Erkenschwick | 4:0 | |
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| 20. Round | 16/03/2017 | FC Gütersloh 2000 | - | TSV Marl-Hüls | 2:2 | ||||
| 29. Round | 23/04/2017 | FC Gütersloh 2000 | - | FC Brünninghausen | 1:1 | ||||
| 31. Round | 05/05/2017 | FC Gütersloh 2000 | - | SC Paderborn 07 II | 3:1 | |
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| 32. Round | 14/05/2017 | SuS Stadtlohn | - | FC Gütersloh 2000 | 1:1 | |
Germany