| 1. Round | 22/08/1998 | Panathinaikos | - | Paniliakos Pyrgos | 2:1 | ||||
| 2. Round | 29/08/1998 | AO Proodeftiki | - | Panathinaikos | 1:2 | ||||
| 3. Round | 12/09/1998 | Panathinaikos | - | Ethnikos Asteras | 4:1 | ||||
| 4. Round | 19/09/1998 | PAOK Saloniki | - | Panathinaikos | 2:0 | ||||
| 5. Round | 25/09/1998 | Panathinaikos | - | Ionikos Nikea | 2:1 | ||||
| 7. Round | 25/10/1998 | Panathinaikos | - | AO Kavala | 6:2 | ||||
| 8. Round | 30/10/1998 | Panathinaikos | - | Panionios GSS | 2:1 | ||||
| 9. Round | 07/11/1998 | Ethnikos Piraeus | - | Panathinaikos | 0:0 | ||||
| 10. Round | 20/11/1998 | Panathinaikos | - | Iraklis Saloniki | 3:2 | ||||
| 11. Round | 28/11/1998 | Skoda Xanthi | - | Panathinaikos | 1:0 | ||||
| 12. Round | 04/12/1998 | Panathinaikos | - | Olympiakos Piraeus | 2:4 | ||||
| 13. Round | 12/12/1998 | AEK Athen | - | Panathinaikos | 2:0 | ||||
| 22. Round | 06/03/1999 | Ionikos Nikea | - | Panathinaikos | 4:4 |  |
|||
| 23. Round | 13/03/1999 | Panathinaikos | - | Aris Saloniki | 3:1 | ||||
| 24. Round | 19/03/1999 | AO Kavala | - | Panathinaikos | 2:1 |
Poland