| 4. Round | 31/07/2016 | Jahn Regensburg II | - | TSV Kottern-St. Mang | 2:1 |  |
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| 6. Round | 07/08/2016 | TSV Schwabmünchen | - | Jahn Regensburg II | 2:0 | ||||
| 7. Round | 14/08/2016 | Jahn Regensburg II | - | FC Ismaning | 0:3 | ||||
| 10. Round | 03/09/2016 | 1. FC Sonthofen | - | Jahn Regensburg II | 3:0 | ||||
| 11. Round | 11/09/2016 | Jahn Regensburg II | - | SV Heimstetten | 1:2 |  |
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| 13. Round | 25/09/2016 | Jahn Regensburg II | - | TSV Landsberg | 4:1 |  |
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| 14. Round | 01/10/2016 | TSV 1883 Bogen | - | Jahn Regensburg II | 2:5 | ||||
| 16. Round | 15/10/2016 | SV Pullach | - | Jahn Regensburg II | 2:2 | |
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| 17. Round | 23/10/2016 | Jahn Regensburg II | - | TSV 1865 Dachau | 0:1 | ||||
| 18. Round | 30/10/2016 | Jahn Regensburg II | - | SV Kirchanschöring | 5:0 | |
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| 19. Round | 05/11/2016 | TSV 1896 Rain | - | Jahn Regensburg II | 3:0 | ||||
| 20. Round | 13/11/2016 | Jahn Regensburg II | - | FC Gundelfingen | 4:1 | |
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| 32. Round | 06/05/2017 | FC Unterföhring | - | Jahn Regensburg II | 2:0 |
Germany