| 4. Round | 28/09/2008 | Iraklis Saloniki | - | Panthrakikos | 0:0 | ||||
| 5. Round | 05/10/2008 | Panthrakikos | - | Panionios GSS | 1:0 | ||||
| 6. Round | 19/10/2008 | Olympiakos Piraeus | - | Panthrakikos | 2:0 | ||||
| 7. Round | 25/10/2008 | AE Lárissa | - | Panthrakikos | 1:2 | ||||
| 8. Round | 02/11/2008 | Panthrakikos | - | Thrasyvoulos Fylis | 1:0 | ||||
| 9. Round | 09/11/2008 | Asteras Tripolis | - | Panthrakikos | 0:0 | ||||
| 10. Round | 16/11/2008 | Panthrakikos | - | Skoda Xanthi | 0:0 | ||||
| 11. Round | 22/11/2008 | Panserraikos | - | Panthrakikos | 1:2 |  |
|||
| 12. Round | 30/11/2008 | Panthrakikos | - | OFI Heraklion | 2:0 | ||||
| 13. Round | 07/12/2008 | AEK Athen | - | Panthrakikos | 1:0 | ||||
| 14. Round | 14/12/2008 | Levadiakos | - | Panthrakikos | 2:0 | ||||
| 15. Round | 21/12/2008 | Panthrakikos | - | Aris Saloniki | 0:0 |  |
|||
| 17. Round | 10/01/2009 | Panthrakikos | - | Panathinaikos | 1:3 | |
|||
| 19. Round | 25/01/2009 | Panthrakikos | - | Iraklis Saloniki | 1:0 | |
|||
| 20. Round | 01/02/2009 | Panionios GSS | - | Panthrakikos | 3:0 | ||||
| 21. Round | 07/02/2009 | Panthrakikos | - | Olympiakos Piraeus | 0:2 | ||||
| 22. Round | 15/02/2009 | Panthrakikos | - | AE Lárissa | 0:1 | ||||
| 27. Round | 22/03/2009 | OFI Heraklion | - | Panthrakikos | 4:3 | |
Brazil