| 2. Round | 13/09/2008 | Panathinaikos | - | Panthrakikos | 3:0 | ||||
| 3. Round | 20/09/2008 | Panthrakikos | - | PAOK Saloniki | 0:1 | ||||
| 4. Round | 28/09/2008 | Iraklis Saloniki | - | Panthrakikos | 0:0 | ||||
| 5. Round | 05/10/2008 | Panthrakikos | - | Panionios GSS | 1:0 | ||||
| 7. Round | 25/10/2008 | AE Lárissa | - | Panthrakikos | 1:2 | ||||
| 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 | ||||
| 13. Round | 07/12/2008 | AEK Athen | - | Panthrakikos | 1:0 | ||||
| 21. Round | 07/02/2009 | Panthrakikos | - | Olympiakos Piraeus | 0:2 | ||||
| 22. Round | 15/02/2009 | Panthrakikos | - | AE Lárissa | 0:1 | ||||
| 29. Round | 12/04/2009 | Panthrakikos | - | Levadiakos | 1:3 | ||||
| 30. Round | 26/04/2009 | Aris Saloniki | - | Panthrakikos | 3:2 |
Greece