| 3. Round | 15/09/2012 | Panthrakikos | - | Panathinaikos | 1:0 | ||||
| 4. Round | 23/09/2012 | Olympiakos Piraeus | - | Panthrakikos | 4:1 | ||||
| 6. Round | 08/10/2012 | Levadiakos | - | Panthrakikos | 0:3 | ||||
| 10. Round | 11/11/2012 | Panthrakikos | - | Asteras Tripolis | 1:0 | ||||
| 11. Round | 18/11/2012 | Skoda Xanthi | - | Panthrakikos | 0:0 | ||||
| 12. Round | 26/11/2012 | Panthrakikos | - | Aris Saloniki | 4:0 | ||||
| 13. Round | 02/12/2012 | OFI Heraklion | - | Panthrakikos | 1:1 | ||||
| 14. Round | 10/12/2012 | Panthrakikos | - | AEK Athen | 1:0 | ||||
| 15. Round | 15/12/2012 | AO Kerkyra | - | Panthrakikos | 0:2 | ||||
| 16. Round | 06/01/2013 | Panthrakikos | - | PAOK Saloniki | 1:4 |  |
|||
| 18. Round | 19/01/2013 | Panathinaikos | - | Panthrakikos | 1:1 | ||||
| 19. Round | 27/01/2013 | Panthrakikos | - | Olympiakos Piraeus | 0:1 | ||||
| 20. Round | 03/02/2013 | Veria FC | - | Panthrakikos | 2:0 | ||||
| 25. Round | 09/03/2013 | Asteras Tripolis | - | Panthrakikos | 1:0 | ||||
| 26. Round | 18/03/2013 | Panthrakikos | - | Skoda Xanthi | 0:2 | ||||
| 27. Round | 30/03/2013 | Aris Saloniki | - | Panthrakikos | 0:0 |  |
|||
| 28. Round | 07/04/2013 | Panthrakikos | - | OFI Heraklion | 3:1 | ||||
| 29. Round | 13/04/2013 | AEK Athen | - | Panthrakikos | 0:3 dec. |
Greece