| 3. Round | 15/09/2012 | Panthrakikos | - | Panathinaikos | 1:0 |  |
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| 4. Round | 23/09/2012 | Olympiakos Piraeus | - | Panthrakikos | 4:1 | ||||
| 6. Round | 08/10/2012 | Levadiakos | - | Panthrakikos | 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 | |
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| 25. Round | 09/03/2013 | Asteras Tripolis | - | Panthrakikos | 1:0 | ||||
| 27. Round | 30/03/2013 | Aris Saloniki | - | Panthrakikos | 0:0 | |
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| 28. Round | 07/04/2013 | Panthrakikos | - | OFI Heraklion | 3:1 |
Greece