| 14. Round | 08/10/2016 | SpVgg Bayreuth | - | Wacker Burghausen | 1:3 | ||||
| 15. Round | 15/10/2016 | Wacker Burghausen | - | TSV 1860 München II | 0:1 | ||||
| 16. Round | 23/10/2016 | TSV 1860 Rosenheim | - | Wacker Burghausen | 1:2 | ||||
| 17. Round | 29/10/2016 | Wacker Burghausen | - | VfR Garching | 3:1 | ||||
| 22. Round | 03/03/2017 | 1. FC Schweinfurt 05 | - | Wacker Burghausen | 1:2 | ||||
| 26. Round | 01/04/2017 | SpVgg Bayern Hof | - | Wacker Burghausen | 0:1 | ||||
| 31. Round | 28/04/2017 | Wacker Burghausen | - | SpVgg Bayreuth | 1:0 | ||||
| 32. Round | 06/05/2017 | TSV 1860 München II | - | Wacker Burghausen | 2:2 | ||||
| 29. Round | 09/05/2017 | FC Ingolstadt 04 II | - | Wacker Burghausen | 6:0 | ||||
| 33. Round | 13/05/2017 | Wacker Burghausen | - | TSV 1860 Rosenheim | 0:1 | ||||
| 34. Round | 20/05/2017 | VfR Garching | - | Wacker Burghausen | 4:0 |
Austria