| 1. Round | 14/08/2016 | FC Carl Zeiss Jena [Youth] | - | FC St. Pauli [Youth] | 2:2 | ||||
| 3. Round | 20/08/2016 | FC Carl Zeiss Jena [Youth] | - | Hertha BSC [Youth] | 3:8 | ||||
| 4. Round | 27/08/2016 | Hannover 96 [Youth] | - | FC Carl Zeiss Jena [Youth] | 2:0 | ||||
| 5. Round | 10/09/2016 | FC Carl Zeiss Jena [Youth] | - | Hamburger SV [Youth] | 1:5 | ||||
| 6. Round | 18/09/2016 | Holstein Kiel [Youth] | - | FC Carl Zeiss Jena [Youth] | 4:0 | ||||
| 26. Round | 06/05/2017 | RB Leipzig [Youth] | - | FC Carl Zeiss Jena [Youth] | 5:1 |
Russia