| 1. Round | 30/08/2008 | Panthrakikos | - | Ergotelis | 1:2 | ||||
| 2. Round | 13/09/2008 | Panathinaikos | - | Panthrakikos | 3:0 | ||||
| 3. Round | 20/09/2008 | Panthrakikos | - | PAOK Saloniki | 0:1 | ||||
| 4. Round | 28/09/2008 | Iraklis Saloniki | - | Panthrakikos | 0:0 | ||||
| 8. Round | 02/11/2008 | Panthrakikos | - | Thrasyvoulos Fylis | 1:0 | ||||
| 16. Round | 03/01/2009 | Ergotelis | - | Panthrakikos | 0:1 |  |
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| 17. Round | 10/01/2009 | Panthrakikos | - | Panathinaikos | 1:3 | |
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| 18. Round | 18/01/2009 | PAOK Saloniki | - | Panthrakikos | 2:0 | ||||
| 20. Round | 01/02/2009 | Panionios GSS | - | Panthrakikos | 3:0 | ||||
| 21. Round | 07/02/2009 | Panthrakikos | - | Olympiakos Piraeus | 0:2 | ||||
| 30. Round | 26/04/2009 | Aris Saloniki | - | Panthrakikos | 3:2 |
Cyprus