| 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 | ||||
| 17. Round | 12/11/2016 | Viktoria Köln | - | Bonner SC | 5:0 | ||||
| 18. Round | 25/11/2016 | Fortuna Düsseldorf II | - | Bonner SC | 3:0 |  |
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| 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 | ||||
| 21. Round | 18/02/2017 | Rot Weiss Ahlen | - | Bonner SC | 1:1 | ||||
| 24. Round | 11/03/2017 | Borussia Dortmund II | - | Bonner SC | 2:0 | ||||
| 25. Round | 19/03/2017 | Bonner SC | - | FC Schalke 04 II | 0:0 | ||||
| 27. Round | 01/04/2017 | Bonner SC | - | Sportfreunde Siegen | 4:2 | ||||
| 28. Round | 08/04/2017 | SG Wattenscheid 09 | - | Bonner SC | 3:0 | ||||
| 29. Round | 13/04/2017 | Bonner SC | - | Rot-Weiß Oberhausen | 2:5 | ||||
| 30. Round | 22/04/2017 | TSG Sprockhövel | - | Bonner SC | 0:2 | ||||
| 33. Round | 13/05/2017 | Wuppertaler SV | - | Bonner SC | 0:0 | ||||
| 34. Round | 20/05/2017 | Bonner SC | - | Viktoria Köln | 2:0 |
Germany