| 1. Round | 22/08/1998 | Apollon Smyrnis | - | Olympiakos Piraeus | 2:5 |  |
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| 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 | |
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| 6. Round | 03/10/1998 | Apollon Smyrnis | - | OFI Heraklion | 1:0 | ||||
| 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 | ||||
| 19. Round | 13/02/1999 | Apollon Smyrnis | - | AEK Athen | 1:1 | ||||
| 20. Round | 20/02/1999 | Apollon Smyrnis | - | Panionios GSS | 0:0 | ||||
| 21. Round | 27/02/1999 | Panelefsiniakos Elefsinas | - | Apollon Smyrnis | 1:0 | |
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| 22. Round | 05/03/1999 | Apollon Smyrnis | - | Veria FC | 2:0 | ||||
| 27. Round | 24/04/1999 | PAOK Saloniki | - | Apollon Smyrnis | 3:1 | |
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| 31. Round | 15/05/1999 | Apollon Smyrnis | - | Panathinaikos | 1:3 | ||||
| 34. Round | 29/05/1999 | Skoda Xanthi | - | Apollon Smyrnis | 1:0 |
Greece