| 3. Round | 20/08/2016 | FC Carl Zeiss Jena [Youth] | - | Hertha BSC [Youth] | 3:8 | ||||
| 6. Round | 18/09/2016 | Holstein Kiel [Youth] | - | FC Carl Zeiss Jena [Youth] | 4:0 | ||||
| 7. Round | 24/09/2016 | FC Carl Zeiss Jena [Youth] | - | Dynamo Dresden [Youth] | 0:1 | ||||
| 8. Round | 15/10/2016 | Eintracht Braunschweig [Youth] | - | FC Carl Zeiss Jena [Youth] | 5:0 | ||||
| 9. Round | 23/10/2016 | FC Carl Zeiss Jena [Youth] | - | JFV Nordwest [Youth] | 1:0 | ||||
| 10. Round | 28/10/2016 | VfL Wolfsburg [Youth] | - | FC Carl Zeiss Jena [Youth] | 3:0 |  |
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| 11. Round | 05/11/2016 | FC Carl Zeiss Jena [Youth] | - | Energie Cottbus [Youth] | 4:0 | |
Germany