| 1. Round | 31/08/2008 | AE Lárissa | - | Thrasyvoulos Fylis | 3:0 |  |
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| 2. Round | 14/09/2008 | Levadiakos | - | Thrasyvoulos Fylis | 1:0 | ||||
| 3. Round | 21/09/2008 | Thrasyvoulos Fylis | - | Asteras Tripolis | 0:2 | |
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| 4. Round | 28/09/2008 | Skoda Xanthi | - | Thrasyvoulos Fylis | 1:0 | |
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| 5. Round | 05/10/2008 | Thrasyvoulos Fylis | - | Panserraikos | 0:1 | ||||
| 6. Round | 19/10/2008 | OFI Heraklion | - | Thrasyvoulos Fylis | 1:3 | ||||
| 7. Round | 26/10/2008 | Thrasyvoulos Fylis | - | AEK Athen | 3:3 | ||||
| 8. Round | 02/11/2008 | Panthrakikos | - | Thrasyvoulos Fylis | 1:0 | ||||
| 9. Round | 09/11/2008 | Thrasyvoulos Fylis | - | Aris Saloniki | 1:2 |  |
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| 10. Round | 16/11/2008 | Ergotelis | - | Thrasyvoulos Fylis | 1:2 | |
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| 12. Round | 29/11/2008 | Thrasyvoulos Fylis | - | PAOK Saloniki | 1:2 | ||||
| 13. Round | 07/12/2008 | Iraklis Saloniki | - | Thrasyvoulos Fylis | 1:1 | |
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| 14. Round | 14/12/2008 | Thrasyvoulos Fylis | - | Panionios GSS | 1:3 | ||||
| 15. Round | 21/12/2008 | Olympiakos Piraeus | - | Thrasyvoulos Fylis | 2:1 | |
Greece