| 1. Round | 30/08/2008 | OFI Heraklion | - | PAOK Saloniki | 0:2 | ||||
| 2. Round | 13/09/2008 | Iraklis Saloniki | - | OFI Heraklion | 1:1 | ||||
| 3. Round | 21/09/2008 | Panionios GSS | - | OFI Heraklion | 1:1 |  |
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| 7. Round | 25/10/2008 | Asteras Tripolis | - | OFI Heraklion | 2:2 | |
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| 8. Round | 02/11/2008 | OFI Heraklion | - | Skoda Xanthi | 0:2 | ||||
| 9. Round | 08/11/2008 | Panserraikos | - | OFI Heraklion | 1:2 | ||||
| 11. Round | 23/11/2008 | OFI Heraklion | - | AEK Athen | 1:1 | ||||
| 12. Round | 30/11/2008 | Panthrakikos | - | OFI Heraklion | 2:0 | ||||
| 30. Round | 26/04/2009 | Panathinaikos | - | OFI Heraklion | 3:1 |
Greece