| 1. Round | 16/07/2016 | FC Augsburg II | - | 1. FC Nürnberg II | 1:1 | ||||
| 10. Round | 09/09/2016 | TSV 1860 Rosenheim | - | FC Augsburg II | 3:0 | ||||
| 14. Round | 07/10/2016 | Bayern München II | - | FC Augsburg II | 0:0 | ||||
| 15. Round | 15/10/2016 | SpVgg Bayern Hof | - | FC Augsburg II | 0:4 |  |
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| 9. Round | 19/10/2016 | FC Augsburg II | - | TSV 1860 München II | 1:0 | ||||
| 16. Round | 22/10/2016 | FC Augsburg II | - | SV Schalding-Heining | 3:0 | ||||
| 17. Round | 29/10/2016 | 1. FC Schweinfurt 05 | - | FC Augsburg II | 1:1 |  |
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| 18. Round | 05/11/2016 | 1. FC Nürnberg II | - | FC Augsburg II | 1:4 | |
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| 19. Round | 12/11/2016 | FC Augsburg II | - | FV Illertissen | 2:0 | |
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| 20. Round | 18/11/2016 | FC Augsburg II | - | Wacker Burghausen | 0:1 | ||||
| 21. Round | 26/11/2016 | TSV Buchbach | - | FC Augsburg II | 2:1 | ||||
| 22. Round | 04/03/2017 | FC Augsburg II | - | SpVgg Unterhaching | 0:1 | ||||
| 24. Round | 18/03/2017 | TSV 1860 München II | - | FC Augsburg II | 1:0 | ||||
| 25. Round | 25/03/2017 | FC Augsburg II | - | SpVgg Bayreuth | 0:2 | ||||
| 26. Round | 01/04/2017 | FC Augsburg II | - | TSV 1860 Rosenheim | 4:1 | ||||
| 27. Round | 08/04/2017 | VfR Garching | - | FC Augsburg II | 0:0 |
Germany