| 1. Round | 31/08/2008 | Aris Saloniki | - | Levadiakos | 2:0 |  |
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| 2. Round | 14/09/2008 | Ergotelis | - | Aris Saloniki | 3:0 | ||||
| 6. Round | 18/10/2008 | Panionios GSS | - | Aris Saloniki | 2:1 | ||||
| 9. Round | 09/11/2008 | Thrasyvoulos Fylis | - | Aris Saloniki | 1:2 | ||||
| 10. Round | 15/11/2008 | Aris Saloniki | - | Asteras Tripolis | 1:1 | ||||
| 12. Round | 30/11/2008 | Aris Saloniki | - | Panserraikos | 2:0 | ||||
| 13. Round | 06/12/2008 | OFI Heraklion | - | Aris Saloniki | 0:1 | ||||
| 14. Round | 14/12/2008 | Aris Saloniki | - | AEK Athen | 1:1 | ||||
| 16. Round | 04/01/2009 | Levadiakos | - | Aris Saloniki | 2:0 | ||||
| 17. Round | 11/01/2009 | Aris Saloniki | - | Ergotelis | 0:0 | ||||
| 20. Round | 31/01/2009 | Iraklis Saloniki | - | Aris Saloniki | 0:1 | ||||
| 21. Round | 07/02/2009 | Aris Saloniki | - | Panionios GSS | 1:0 | ||||
| 22. Round | 14/02/2009 | Olympiakos Piraeus | - | Aris Saloniki | 2:1 | ||||
| 23. Round | 22/02/2009 | AE Lárissa | - | Aris Saloniki | 1:1 | ||||
| 24. Round | 28/02/2009 | Aris Saloniki | - | Thrasyvoulos Fylis | 2:1 | |
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| 25. Round | 07/03/2009 | Asteras Tripolis | - | Aris Saloniki | 4:0 | ||||
| 26. Round | 14/03/2009 | Aris Saloniki | - | Skoda Xanthi | 0:1 | ||||
| 30. Round | 26/04/2009 | Aris Saloniki | - | Panthrakikos | 3:2 |
Poland