| 3. Round | 10/09/2016 | Levadiakos | - | Panathinaikos | 0:3 | ||||
| 4. Round | 18/09/2016 | Panathinaikos | - | PAS Giannina | 4:0 | ||||
| 5. Round | 24/09/2016 | Panetolikos | - | Panathinaikos | 0:0 | ||||
| 6. Round | 02/10/2016 | Panathinaikos | - | Asteras Tripolis | 3:1 |  |
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| 8. Round | 24/10/2016 | Veria FC | - | Panathinaikos | 1:1 | ||||
| 9. Round | 30/10/2016 | Panathinaikos | - | AEP Iraklis FC | 2:0 | ||||
| 12. Round | 27/11/2016 | Panionios GSS | - | Panathinaikos | 1:1 | |
Bulgaria