| 5. Round | 20/08/2016 | Rot-Weiß Oberhausen | - | FC Schalke 04 II | 1:1 | ||||
| 9. Round | 17/09/2016 | Wuppertaler SV | - | FC Schalke 04 II | 0:2 |  |
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| 10. Round | 24/09/2016 | FC Schalke 04 II | - | Viktoria Köln | 1:2 | ||||
| 11. Round | 02/10/2016 | Fortuna Düsseldorf II | - | FC Schalke 04 II | 1:0 | ||||
| 13. Round | 15/10/2016 | SV Rödinghausen | - | FC Schalke 04 II | 2:0 | ||||
| 14. Round | 23/10/2016 | FC Schalke 04 II | - | Rot Weiss Ahlen | 3:1 | ||||
| 15. Round | 29/10/2016 | SC Verl | - | FC Schalke 04 II | 2:1 |  |
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| 19. Round | 03/12/2016 | 1. FC Köln II | - | FC Schalke 04 II | 2:1 | ||||
| 21. Round | 19/02/2017 | SG Wattenscheid 09 | - | FC Schalke 04 II | 2:1 | ||||
| 24. Round | 11/03/2017 | FC Schalke 04 II | - | SC Wiedenbrück | 1:2 |  |
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| 30. Round | 23/04/2017 | FC Schalke 04 II | - | SV Rödinghausen | 1:1 | ||||
| 31. Round | 28/04/2017 | Rot Weiss Ahlen | - | FC Schalke 04 II | 2:1 | |
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| 32. Round | 06/05/2017 | FC Schalke 04 II | - | SC Verl | 0:0 | |
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| 22. Round | 10/05/2017 | FC Schalke 04 II | - | Rot-Weiß Oberhausen | 0:1 | ||||
| 33. Round | 13/05/2017 | Alemannia Aachen | - | FC Schalke 04 II | 3:2 |
Germany