| 21. Round | 04/02/2017 | 1. FSV Mainz 05 II | - | SC Paderborn 07 | 0:1 | ||||
| 22. Round | 10/02/2017 | VfL Osnabrück | - | 1. FSV Mainz 05 II | 1:2 |  |
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| 23. Round | 17/02/2017 | 1. FSV Mainz 05 II | - | MSV Duisburg | 0:2 | ||||
| 25. Round | 04/03/2017 | 1. FC Magdeburg | - | 1. FSV Mainz 05 II | 1:2 | ||||
| 26. Round | 11/03/2017 | 1. FSV Mainz 05 II | - | Werder Bremen II | 0:1 | ||||
| 27. Round | 15/03/2017 | SV Wehen Wiesbaden | - | 1. FSV Mainz 05 II | 0:2 |  |
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| 28. Round | 18/03/2017 | 1. FSV Mainz 05 II | - | Holstein Kiel | 0:3 | |
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| 29. Round | 25/03/2017 | Rot-Weiß Erfurt | - | 1. FSV Mainz 05 II | 0:0 | ||||
| 30. Round | 31/03/2017 | 1. FSV Mainz 05 II | - | Chemnitzer FC | 0:1 | ||||
| 31. Round | 04/04/2017 | Jahn Regensburg | - | 1. FSV Mainz 05 II | 2:1 | ||||
| 32. Round | 09/04/2017 | 1. FSV Mainz 05 II | - | Hansa Rostock | 2:4 | ||||
| 34. Round | 22/04/2017 | 1. FSV Mainz 05 II | - | Hallescher FC | 3:2 | |
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| 35. Round | 29/04/2017 | FSV Frankfurt | - | 1. FSV Mainz 05 II | 1:2 | |
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| 36. Round | 06/05/2017 | 1. FSV Mainz 05 II | - | VfR Aalen | 2:0 | |
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| 37. Round | 13/05/2017 | Sportfreunde Lotte | - | 1. FSV Mainz 05 II | 3:3 | |
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Bosnia-Herzegovina