| 1. Round | 22/08/1998 | OFI Heraklion | - | Ethnikos Piraeus | 3:0 | ||||
| 2. Round | 29/08/1998 | Iraklis Saloniki | - | OFI Heraklion | 3:0 |  |
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| 3. Round | 12/09/1998 | OFI Heraklion | - | Skoda Xanthi | 4:2 | ||||
| 4. Round | 19/09/1998 | Olympiakos Piraeus | - | OFI Heraklion | 3:0 | ||||
| 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 | ||||
| 8. Round | 31/10/1998 | Veria FC | - | OFI Heraklion | 0:0 | ||||
| 9. Round | 07/11/1998 | Panionios GSS | - | OFI Heraklion | 0:1 | ||||
| 10. Round | 21/11/1998 | OFI Heraklion | - | Paniliakos Pyrgos | 3:1 | ||||
| 22. Round | 06/03/1999 | AEK Athen | - | OFI Heraklion | 2:0 | ||||
| 26. Round | 17/04/1999 | OFI Heraklion | - | Panionios GSS | 2:0 | ||||
| 27. Round | 23/04/1999 | Paniliakos Pyrgos | - | OFI Heraklion | 1:2 | |
Greece