| 1. Round | 31/08/2008 | Panionios GSS | - | Skoda Xanthi | 0:1 | ||||
| 3. Round | 21/09/2008 | Panionios GSS | - | OFI Heraklion | 1:1 | ||||
| 4. Round | 28/09/2008 | Panionios GSS | - | AEK Athen | 2:2 | ||||
| 5. Round | 05/10/2008 | Panthrakikos | - | Panionios GSS | 1:0 |  |
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| 6. Round | 18/10/2008 | Panionios GSS | - | Aris Saloniki | 2:1 | ||||
| 7. Round | 26/10/2008 | Ergotelis | - | Panionios GSS | 2:5 |  |
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| 8. Round | 01/11/2008 | Panionios GSS | - | Panathinaikos | 1:2 | ||||
| 13. Round | 07/12/2008 | Panionios GSS | - | AE Lárissa | 1:1 | ||||
| 18. Round | 18/01/2009 | OFI Heraklion | - | Panionios GSS | 2:0 |
Greece