| 1. Round | 31/08/2008 | AEK Athen | - | Panathinaikos | 2:1 | ||||
| 2. Round | 13/09/2008 | Panathinaikos | - | Panthrakikos | 3:0 |  |
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| 3. Round | 20/09/2008 | Aris Saloniki | - | Panathinaikos | 1:2 | |
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| 5. Round | 05/10/2008 | Panathinaikos | - | Levadiakos | 2:0 |  |
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| 6. Round | 19/10/2008 | PAOK Saloniki | - | Panathinaikos | 0:0 | |
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| 7. Round | 26/10/2008 | Panathinaikos | - | Iraklis Saloniki | 2:2 | ||||
| 11. Round | 22/11/2008 | Panathinaikos | - | Thrasyvoulos Fylis | 3:0 | |
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| 12. Round | 29/11/2008 | Panathinaikos | - | Asteras Tripolis | 1:1 | |
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| 15. Round | 21/12/2008 | OFI Heraklion | - | Panathinaikos | 0:3 | ||||
| 17. Round | 10/01/2009 | Panthrakikos | - | Panathinaikos | 1:3 | ||||
| 20. Round | 01/02/2009 | Levadiakos | - | Panathinaikos | 1:2 | |
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| 23. Round | 21/02/2009 | Panathinaikos | - | Panionios GSS | 2:1 | ||||
| 24. Round | 01/03/2009 | Olympiakos Piraeus | - | Panathinaikos | 0:0 | ||||
| 25. Round | 07/03/2009 | Panathinaikos | - | AE Lárissa | 3:0 | ||||
| 28. Round | 05/04/2009 | Panathinaikos | - | Skoda Xanthi | 2:0 | |
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| 29. Round | 12/04/2009 | Panserraikos | - | Panathinaikos | 0:0 | |
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| 30. Round | 26/04/2009 | Panathinaikos | - | OFI Heraklion | 3:1 |
Austria