| 3. Round | 12/09/1998 | AO Kavala | - | PAOK Saloniki | 1:1 | ||||
| 4. Round | 19/09/1998 | PAOK Saloniki | - | Panathinaikos | 2:0 |  |
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| 6. Round | 03/10/1998 | PAOK Saloniki | - | Iraklis Saloniki | 2:1 | ||||
| 7. Round | 24/10/1998 | Skoda Xanthi | - | PAOK Saloniki | 0:1 | ||||
| 9. Round | 07/11/1998 | PAOK Saloniki | - | AEK Athen | 2:1 | ||||
| 10. Round | 21/11/1998 | Apollon Smyrnis | - | PAOK Saloniki | 1:4 | ||||
| 11. Round | 28/11/1998 | PAOK Saloniki | - | Panelefsiniakos Elefsinas | 3:1 | ||||
| 12. Round | 04/12/1998 | Veria FC | - | PAOK Saloniki | 1:2 | ||||
| 13. Round | 12/12/1998 | PAOK Saloniki | - | OFI Heraklion | 3:1 | ||||
| 14. Round | 19/12/1998 | Paniliakos Pyrgos | - | PAOK Saloniki | 1:2 | ||||
| 17. Round | 29/01/1999 | Panionios GSS | - | PAOK Saloniki | 0:1 | ||||
| 18. Round | 06/02/1999 | PAOK Saloniki | - | Ionikos Nikea | 0:0 | ||||
| 19. Round | 14/02/1999 | Aris Saloniki | - | PAOK Saloniki | 2:0 | ||||
| 25. Round | 03/04/1999 | Olympiakos Piraeus | - | PAOK Saloniki | 2:1 | ||||
| 26. Round | 17/04/1999 | AEK Athen | - | PAOK Saloniki | 2:0 | ||||
| 33. Round | 22/05/1999 | PAOK Saloniki | - | Ethnikos Asteras | 5:1 | ||||
| 34. Round | 29/05/1999 | PAOK Saloniki | - | Panionios GSS | 3:0 |
Greece