| 1. Round | 22/08/1998 | OFI Heraklion | - | Ethnikos Piraeus | 3:0 | ||||
| 2. Round | 29/08/1998 | Iraklis Saloniki | - | OFI Heraklion | 3:0 | ||||
| 3. Round | 12/09/1998 | OFI Heraklion | - | Skoda Xanthi | 4:2 | ||||
| 5. Round | 25/09/1998 | OFI Heraklion | - | AEK Athen | 0:1 | ||||
| 6. Round | 03/10/1998 | Apollon Smyrnis | - | OFI Heraklion | 1:0 | ||||
| 7. Round | 24/10/1998 | OFI Heraklion | - | Panelefsiniakos Elefsinas | 3:0 | ||||
| 9. Round | 07/11/1998 | Panionios GSS | - | OFI Heraklion | 0:1 | ||||
| 10. Round | 21/11/1998 | OFI Heraklion | - | Paniliakos Pyrgos | 3:1 |  |
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| 11. Round | 28/11/1998 | AO Proodeftiki | - | OFI Heraklion | 0:1 | |
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| 12. Round | 05/12/1998 | OFI Heraklion | - | Ethnikos Asteras | 1:1 | ||||
| 13. Round | 12/12/1998 | PAOK Saloniki | - | OFI Heraklion | 3:1 | ||||
| 14. Round | 19/12/1998 | OFI Heraklion | - | Ionikos Nikea | 2:1 | ||||
| 15. Round | 15/01/1999 | Aris Saloniki | - | OFI Heraklion | 3:1 | ||||
| 16. Round | 22/01/1999 | OFI Heraklion | - | AO Kavala | 4:0 |
Poland