| 3. Round | 09/08/2016 | Bonner SC | - | SV Rödinghausen | 3:2 | ||||
| 4. Round | 14/08/2016 | Bonner SC | - | Rot Weiss Ahlen | 3:1 | ||||
| 5. Round | 20/08/2016 | Bonner SC | - | SC Verl | 1:0 | ||||
| 6. Round | 26/08/2016 | Alemannia Aachen | - | Bonner SC | 3:2 |  |
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| 8. Round | 10/09/2016 | FC Schalke 04 II | - | Bonner SC | 0:5 | ||||
| 9. Round | 17/09/2016 | Bonner SC | - | 1. FC Köln II | 2:3 | |
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| 7. Round | 20/09/2016 | Bonner SC | - | Borussia Dortmund II | 2:2 | ||||
| 10. Round | 24/09/2016 | Sportfreunde Siegen | - | Bonner SC | 2:2 |  |
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| 13. Round | 15/10/2016 | Bonner SC | - | TSG Sprockhövel | 0:2 | ||||
| 14. Round | 22/10/2016 | SC Wiedenbrück | - | Bonner SC | 1:3 | ||||
| 15. Round | 28/10/2016 | Bor. Mönchengladbach II | - | Bonner SC | 1:2 | ||||
| 16. Round | 05/11/2016 | Bonner SC | - | Wuppertaler SV | 3:0 | ||||
| 19. Round | 04/12/2016 | Bonner SC | - | Rot-Weiss Essen | 1:2 | ||||
| 20. Round | 10/12/2016 | SV Rödinghausen | - | Bonner SC | 3:2 | ||||
| 26. Round | 13/02/2017 | 1. FC Köln II | - | Bonner SC | 2:0 | ||||
| 22. Round | 25/02/2017 | SC Verl | - | Bonner SC | 0:1 |
Germany