| Competition: | Alpha Ethniki |
| Season: | 1998–99 |
| Winners: | Olympiacos 28th Greek title |
| Relegated: | Panelefsiniakos Veria Ethnikos Piraeus |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Olympiacos AEK Athens |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | Panathinaikos PAOK Ionikos Aris |
| League Topscorer: | Demis Nikolaidis (22 goals) |
| Matches: | 306 |
| Total Goals: | 832 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
The 1998–99 Alpha Ethniki was the 63rd season of the highest football league of Greece. The season began on 22 August 1998 and ended on 30 May 1999. Olympiacos won their third consecutive and 28th Greek title.
| Rank | Player | Club | Goals | |
|---|---|---|---|---|
| 1 | Demis Nikolaidis | AEK Athens | 22 | |
| 2 | Nikos Frousos | Ionikos | 18 | |
| 3 |  Leszek Pisz | Kavala | 14 | |
 Ismail Ba | Skoda Xanthi | |||
| 5 | Nikos Liberopoulos | Panathinaikos | 13 | |
| Christos Maladenis | AEK Athens | |||
 Paulo Andrioli | Ionikos / Aris | |||
| 8 | Grigoris Georgatos | Olympiacos | 12 | |
| Krzysztof Warzycha | Panathinaikos | |||
| 10 | Apostolos Liolidis | Aris | 11 |
Annual awards were announced on 1 December 1999.[1]
| Award | Winner | Club | |
|---|---|---|---|
| Greek Player of the Season | Grigoris Georgatos | Olympiacos | |
| Foreign Player of the Season |  Siniša Gogić | Olympiacos | |
| Young Player of the Season | Nikos Iordanidis | OFI | |
| Goalkeeper of the Season | Ilias Atmatsidis | AEK Athens | |
| Golden Boot | Demis Nikolaidis | AEK Athens | |
| Manager of the Season |  Dušan Bajević | Olympiacos |
