| 4. Round | 18/09/2016 | Panathinaikos | - | PAS Giannina | 4:0 |  |
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| 5. Round | 24/09/2016 | Panetolikos | - | Panathinaikos | 0:0 | ||||
| 6. Round | 02/10/2016 | Panathinaikos | - | Asteras Tripolis | 3:1 | ||||
| 10. Round | 06/11/2016 | Olympiakos Piraeus | - | Panathinaikos | 3:0 | ||||
| 13. Round | 04/12/2016 | Panathinaikos | - | PAOK Saloniki | 1:0 | |
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| 14. Round | 11/12/2016 | Atromitos | - | Panathinaikos | 0:1 | ||||
| 15. Round | 18/12/2016 | AE Lárissa | - | Panathinaikos | 0:0 | ||||
| 19. Round | 04/02/2017 | PAS Giannina | - | Panathinaikos | 1:1 | ||||
| 20. Round | 12/02/2017 | Panathinaikos | - | Panetolikos | 4:0 | ||||
| 21. Round | 18/02/2017 | Asteras Tripolis | - | Panathinaikos | 0:5 | ||||
| 22. Round | 25/02/2017 | Xanthi FC | - | Panathinaikos | 1:0 | ||||
| 23. Round | 04/03/2017 | Panathinaikos | - | Veria FC | 5:0 | ||||
| 24. Round | 11/03/2017 | AEP Iraklis FC | - | Panathinaikos | 1:1 | ||||
| 25. Round | 19/03/2017 | Panathinaikos | - | Olympiakos Piraeus | 1:0 | ||||
| 26. Round | 02/04/2017 | AEK Athen | - | Panathinaikos | 2:3 | ||||
| 27. Round | 06/04/2017 | Panathinaikos | - | Panionios GSS | 1:0 | ||||
| 29. Round | 23/04/2017 | Panathinaikos | - | Atromitos | 1:0 |
France