| 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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| 4. Round | 19/09/1998 | Olympiakos Piraeus | - | OFI Heraklion | 3:0 | ||||
| 7. Round | 24/10/1998 | OFI Heraklion | - | Panelefsiniakos Elefsinas | 3:0 | ||||
| 9. Round | 07/11/1998 | Panionios GSS | - | OFI Heraklion | 0:1 | ||||
| 11. Round | 28/11/1998 | AO Proodeftiki | - | OFI Heraklion | 0:1 | ||||
| 12. Round | 05/12/1998 | OFI Heraklion | - | Ethnikos Asteras | 1:1 | |
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| 13. Round | 12/12/1998 | PAOK Saloniki | - | OFI Heraklion | 3:1 | ||||
| 15. Round | 15/01/1999 | Aris Saloniki | - | OFI Heraklion | 3:1 | ||||
| 17. Round | 29/01/1999 | Panathinaikos | - | OFI Heraklion | 1:0 | |
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| 18. Round | 06/02/1999 | Ethnikos Piraeus | - | OFI Heraklion | 1:3 | |
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| 19. Round | 13/02/1999 | OFI Heraklion | - | Iraklis Saloniki | 3:1 | ||||
| 20. Round | 20/02/1999 | Skoda Xanthi | - | OFI Heraklion | 3:1 | |
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| 23. Round | 13/03/1999 | OFI Heraklion | - | Apollon Smyrnis | 0:1 | |
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| 24. Round | 20/03/1999 | Panelefsiniakos Elefsinas | - | OFI Heraklion | 1:2 |
Greece