| 1. Round | 26/08/2012 | PAOK Saloniki | - | Panthrakikos | 1:0 | ||||
| 2. Round | 01/09/2012 | Platanias Chanion | - | Panthrakikos | 2:0 | ||||
| 4. Round | 23/09/2012 | Olympiakos Piraeus | - | Panthrakikos | 4:1 |  |
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| 5. Round | 30/09/2012 | Panthrakikos | - | Veria FC | 0:1 | ||||
| 6. Round | 08/10/2012 | Levadiakos | - | Panthrakikos | 0:3 | ||||
| 7. Round | 21/10/2012 | Panthrakikos | - | PAS Giannina | 0:3 | ||||
| 8. Round | 27/10/2012 | Panthrakikos | - | Panionios GSS | 1:2 | ||||
| 9. Round | 03/11/2012 | Atromitos | - | Panthrakikos | 2:1 | ||||
| 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 | ||||
| 16. Round | 06/01/2013 | Panthrakikos | - | PAOK Saloniki | 1:4 | ||||
| 17. Round | 12/01/2013 | Panthrakikos | - | Platanias Chanion | 1:1 | ||||
| 18. Round | 19/01/2013 | Panathinaikos | - | Panthrakikos | 1:1 |
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