| 1. Round | 13/08/2016 | Hansa Rostock [Youth B] | - | Eintracht Braunschweig [Youth B] | 1:0 | ||||
| 2. Round | 20/08/2016 | Eintracht Braunschweig [Youth B] | - | Holstein Kiel [Youth B] | 1:1 | ||||
| 3. Round | 28/08/2016 | Eintracht Braunschweig [Youth B] | - | TeBe Berlin [Youth B] | 1:1 |  |
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| 4. Round | 03/09/2016 | Hertha BSC [Youth B] | - | Eintracht Braunschweig [Youth B] | 0:4 | ||||
| 5. Round | 17/09/2016 | Eintracht Braunschweig [Youth B] | - | 1. FC Magdeburg [Youth B] | 1:1 | ||||
| 7. Round | 08/10/2016 | Eintracht Braunschweig [Youth B] | - | RB Leipzig [Youth B] | 0:7 | ||||
| 8. Round | 15/10/2016 | Dynamo Dresden [Youth B] | - | Eintracht Braunschweig [Youth B] | 0:4 | ||||
| 9. Round | 23/10/2016 | Eintracht Braunschweig [Youth B] | - | FC St. Pauli [Youth B] | 2:1 | ||||
| 15. Round | 10/12/2016 | Holstein Kiel [Youth B] | - | Eintracht Braunschweig [Youth B] | 2:2 |
Greece