| Competition: | Alpha Ethniki |
| Season: | 1999–2000 |
| Winners: | Olympiacos 29th Greek title |
| Relegated: | Kavala Proodeftiki Apollon Athens Trikala |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Olympiacos Panathinaikos |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | AEK Athens OFI PAOK Iraklis |
| Continentalcup3: | Intertoto Cup |
| Continentalcup3 Qualifiers: | Kalamata |
| League Topscorer: | Dimitris Nalitzis (24 goals) |
| Matches: | 306 |
| Total Goals: | 885 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Alpha Ethniki was the 64th season of the highest football league of Greece. The season began on 19 September 1999 and ended on 28 May 2000. Olympiacos won their fourth consecutive and 29th Greek title.
AEK Athens qualified through the Cup, the 3rd league UEFA Cup place is decided between the teams within 5 points from 6th to 8th place.
UEFA Cup Play-off
Iraklis with two Home-matches, Aris one, Panionios none
|}
| Rank | Player | Club | Goals |
|---|---|---|---|
| 1 | Dimitris Nalitzis | PAOK | 24 |
| 2 | Nikos Liberopoulos | Panathinaikos | 23 |
| 3 | Demis Nikolaidis | AEK Athens | 22 |
 Michalis Konstantinou | Iraklis | ||
| 5 | Rónald Gómez | OFI | 19 |
| 6 | Alexis Alexandris | Olympiacos | 15 |
| 7 | Predrag Đorđević | Olympiacos | 12 |
| 8 | Nikos Frousos | PAOK | 11 |
| Saša Jovanović | Trikala | ||
| Paraschos Zouboulis | Skoda Xanthi |
Annual awards were announced on 19 December 2000.[1]
| Award | Winner | Club | |
|---|---|---|---|
| Greek Player of the Season | Nikos Liberopoulos | Panathinaikos | |
| Foreign Player of the Season |  Giovanni | Olympiacos | |
| Young Player of the Season | Christos Patsatzoglou Kostas Katsouranis | Skoda Xanthi Panachaiki | |
| Goalkeeper of the Season | Antonios Nikopolidis | Panathinaikos | |
| Golden Boot | Dimitris Nalitzis | PAOK | |
| Manager of the Season | Ioannis Kyrastas | Panathinaikos |
