| 1. Round | 17/09/2000 | AEK Athen | - | Iraklis Saloniki | 2:0 |  |
|||
| 2. Round | 23/09/2000 | Iraklis Saloniki | - | Panachaiki GE | 2:0 | ||||
| 3. Round | 30/09/2000 | PS Kalamata | - | Iraklis Saloniki | 0:0 | |
|||
| 4. Round | 28/10/2000 | Iraklis Saloniki | - | PAS Giannina | 2:1 | |
|||
| 6. Round | 11/11/2000 | Aris Saloniki | - | Iraklis Saloniki | 0:2 | ||||
| 7. Round | 18/11/2000 | Iraklis Saloniki | - | OFI Heraklion | 3:0 | ||||
| 8. Round | 25/11/2000 | Paniliakos Pyrgos | - | Iraklis Saloniki | 1:2 | |
|||
| 9. Round | 02/12/2000 | Iraklis Saloniki | - | Panathinaikos | 0:1 | ||||
| 10. Round | 09/12/2000 | PAOK Saloniki | - | Iraklis Saloniki | 4:2 | ||||
| 24. Round | 31/03/2001 | Panathinaikos | - | Iraklis Saloniki | 2:1 | ||||
| 25. Round | 07/04/2001 | Iraklis Saloniki | - | PAOK Saloniki | 1:1 | |
|||
| 26. Round | 19/04/2001 | Skoda Xanthi | - | Iraklis Saloniki | 1:0 | ||||
| 27. Round | 29/04/2001 | Olympiakos Piraeus | - | Iraklis Saloniki | 3:1 | |
|||
| 30. Round | 25/05/2001 | Iraklis Saloniki | - | Ionikos Nikea | 3:2 |
Albania