| 2. Round | 13/09/2008 | Panathinaikos | - | Panthrakikos | 3:0 | ||||
| 3. Round | 20/09/2008 | Aris Saloniki | - | Panathinaikos | 1:2 |  |
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| 5. Round | 05/10/2008 | Panathinaikos | - | Levadiakos | 2:0 | ||||
| 6. Round | 19/10/2008 | PAOK Saloniki | - | Panathinaikos | 0:0 | |
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| 4. Round | 29/10/2008 | Panathinaikos | - | Ergotelis | 2:3 | |
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| 8. Round | 01/11/2008 | Panionios GSS | - | Panathinaikos | 1:2 | ||||
| 12. Round | 29/11/2008 | Panathinaikos | - | Asteras Tripolis | 1:1 | ||||
| 14. Round | 14/12/2008 | Panathinaikos | - | Panserraikos | 3:0 | ||||
| 15. Round | 21/12/2008 | OFI Heraklion | - | Panathinaikos | 0:3 | ||||
| 17. Round | 10/01/2009 | Panthrakikos | - | Panathinaikos | 1:3 | ||||
| 25. Round | 07/03/2009 | Panathinaikos | - | AE Lárissa | 3:0 | ||||
| 26. Round | 15/03/2009 | Thrasyvoulos Fylis | - | Panathinaikos | 0:1 | ||||
| 28. Round | 05/04/2009 | Panathinaikos | - | Skoda Xanthi | 2:0 | ||||
| 30. Round | 26/04/2009 | Panathinaikos | - | OFI Heraklion | 3:1 |
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