| 1. Round | 22/08/1998 | Ionikos Nikea | - | PAOK Saloniki | 1:0 | ||||
| 2. Round | 29/08/1998 | Ionikos Nikea | - | Panionios GSS | 4:3 |  |
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| 3. Round | 12/09/1998 | Aris Saloniki | - | Ionikos Nikea | 0:0 |  |
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| 5. Round | 25/09/1998 | Panathinaikos | - | Ionikos Nikea | 2:1 | |
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| 6. Round | 03/10/1998 | Ionikos Nikea | - | Ethnikos Piraeus | 5:0 | |
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| 8. Round | 31/10/1998 | Ionikos Nikea | - | Skoda Xanthi | 0:1 | |
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| 9. Round | 08/11/1998 | Olympiakos Piraeus | - | Ionikos Nikea | 2:0 | |
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| 10. Round | 20/11/1998 | AEK Athen | - | Ionikos Nikea | 2:1 | ||||
| 11. Round | 28/11/1998 | Ionikos Nikea | - | Apollon Smyrnis | 3:0 | |
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| 15. Round | 15/01/1999 | Ionikos Nikea | - | Paniliakos Pyrgos | 1:1 |  |
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| 17. Round | 29/01/1999 | Ionikos Nikea | - | Ethnikos Asteras | 5:0 | ||||
| 18. Round | 06/02/1999 | PAOK Saloniki | - | Ionikos Nikea | 0:0 | ||||
| 19. Round | 13/02/1999 | Panionios GSS | - | Ionikos Nikea | 0:2 | ||||
| 20. Round | 19/02/1999 | Ionikos Nikea | - | Aris Saloniki | 3:0 | |
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| 26. Round | 17/04/1999 | Ionikos Nikea | - | Olympiakos Piraeus | 1:3 | |
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| 30. Round | 11/05/1999 | Veria FC | - | Ionikos Nikea | 0:2 | |
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| 31. Round | 15/05/1999 | Ionikos Nikea | - | OFI Heraklion | 2:0 | ||||
| 34. Round | 29/05/1999 | Ethnikos Asteras | - | Ionikos Nikea | 1:1 |
Greece