| 15. Round | 15/01/1999 | Apollon Smyrnis | - | Ethnikos Piraeus | 4:0 |  |
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| 16. Round | 22/01/1999 | Ethnikos Piraeus | - | Panelefsiniakos Elefsinas | 2:2 | |
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| 19. Round | 13/02/1999 | Ethnikos Piraeus | - | Paniliakos Pyrgos | 1:1 | ||||
| 20. Round | 20/02/1999 | AO Proodeftiki | - | Ethnikos Piraeus | 0:0 | ||||
| 21. Round | 27/02/1999 | Ethnikos Piraeus | - | Ethnikos Asteras | 1:2 | ||||
| 22. Round | 06/03/1999 | PAOK Saloniki | - | Ethnikos Piraeus | 0:0 | |
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| 23. Round | 13/03/1999 | Ethnikos Piraeus | - | Ionikos Nikea | 1:2 | ||||
| 24. Round | 20/03/1999 | Aris Saloniki | - | Ethnikos Piraeus | 4:0 | ||||
| 25. Round | 27/03/1999 | Ethnikos Piraeus | - | AO Kavala | 0:2 | ||||
| 26. Round | 18/04/1999 | Panathinaikos | - | Ethnikos Piraeus | 5:1 | ||||
| 27. Round | 25/04/1999 | Panionios GSS | - | Ethnikos Piraeus | 2:0 | |
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| 30. Round | 11/05/1999 | Ethnikos Piraeus | - | Olympiakos Piraeus | 0:3 | ||||
| 31. Round | 15/05/1999 | AEK Athen | - | Ethnikos Piraeus | 2:0 | |
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| 32. Round | 19/05/1999 | Ethnikos Piraeus | - | Apollon Smyrnis | 2:3 | ||||
| 33. Round | 22/05/1999 | Panelefsiniakos Elefsinas | - | Ethnikos Piraeus | 3:0 | ||||
| 34. Round | 29/05/1999 | Ethnikos Piraeus | - | Veria FC | 0:2 |
Greece