| 1. Round | 31/08/2008 | Panionios GSS | - | Skoda Xanthi | 0:1 | ||||
| 2. Round | 13/09/2008 | Skoda Xanthi | - | Olympiakos Piraeus | 0:1 |  |
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| 6. Round | 19/10/2008 | Levadiakos | - | Skoda Xanthi | 0:0 | |
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| 7. Round | 26/10/2008 | Skoda Xanthi | - | Panserraikos | 2:1 | ||||
| 8. Round | 02/11/2008 | OFI Heraklion | - | Skoda Xanthi | 0:2 | |
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| 9. Round | 08/11/2008 | Skoda Xanthi | - | AEK Athen | 1:1 | |
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| 11. Round | 23/11/2008 | Skoda Xanthi | - | Aris Saloniki | 1:1 | ||||
| 12. Round | 30/11/2008 | Ergotelis | - | Skoda Xanthi | 0:0 | |
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| 14. Round | 13/12/2008 | PAOK Saloniki | - | Skoda Xanthi | 1:0 | ||||
| 15. Round | 20/12/2008 | Iraklis Saloniki | - | Skoda Xanthi | 1:0 | ||||
| 17. Round | 10/01/2009 | Olympiakos Piraeus | - | Skoda Xanthi | 2:1 | ||||
| 18. Round | 18/01/2009 | Skoda Xanthi | - | AE Lárissa | 1:1 | |
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| 20. Round | 01/02/2009 | Skoda Xanthi | - | Asteras Tripolis | 0:0 | ||||
| 21. Round | 08/02/2009 | Skoda Xanthi | - | Levadiakos | 4:0 | |
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| 22. Round | 15/02/2009 | Panserraikos | - | Skoda Xanthi | 1:0 | |
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| 25. Round | 08/03/2009 | Skoda Xanthi | - | Panthrakikos | 1:0 | |
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| 26. Round | 14/03/2009 | Aris Saloniki | - | Skoda Xanthi | 0:1 | ||||
| 27. Round | 22/03/2009 | Skoda Xanthi | - | Ergotelis | 0:1 | |
Greece