| 1. Round | 22/08/1998 | Apollon Smyrnis | - | Olympiakos Piraeus | 2:5 | ||||
| 2. Round | 29/08/1998 | AEK Athen | - | Apollon Smyrnis | 3:1 |  |
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| 3. Round | 12/09/1998 | Panionios GSS | - | Apollon Smyrnis | 4:2 | ||||
| 4. Round | 19/09/1998 | Apollon Smyrnis | - | Panelefsiniakos Elefsinas | 1:1 | ||||
| 5. Round | 26/09/1998 | Veria FC | - | Apollon Smyrnis | 1:1 |  |
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| 6. Round | 03/10/1998 | Apollon Smyrnis | - | OFI Heraklion | 1:0 | ||||
| 7. Round | 24/10/1998 | Paniliakos Pyrgos | - | Apollon Smyrnis | 3:1 | ||||
| 8. Round | 31/10/1998 | Apollon Smyrnis | - | AO Proodeftiki | 2:2 | ||||
| 9. Round | 07/11/1998 | Ethnikos Asteras | - | Apollon Smyrnis | 5:1 | ||||
| 10. Round | 21/11/1998 | Apollon Smyrnis | - | PAOK Saloniki | 1:4 | ||||
| 11. Round | 28/11/1998 | Ionikos Nikea | - | Apollon Smyrnis | 3:0 | ||||
| 12. Round | 05/12/1998 | Apollon Smyrnis | - | Aris Saloniki | 1:3 | ||||
| 13. Round | 12/12/1998 | Apollon Smyrnis | - | AO Kavala | 1:1 | |
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| 14. Round | 19/12/1998 | Panathinaikos | - | Apollon Smyrnis | 5:0 |
Greece