| Competition: | Alpha Ethniki |
| Season: | 1968–69 |
| Winners: | Panathinaikos 9th Greek title |
| Relegated: | Apollon Athens Veria Trikala Chalkida AEL Limassol |
| Continentalcup1: | European Cup |
| Continentalcup1 Qualifiers: | Panathinaikos |
| Continentalcup2: | Cup Winners' Cup |
| Continentalcup2 Qualifiers: | Olympiacos |
| Continentalcup3: | Inter-Cities Fairs Cup |
| Continentalcup3 Qualifiers: | Aris Panionios |
| League Topscorer: | Giorgos Sideris (35 goals) |
| Matches: | 306 |
| Total Goals: | 808 |
| Prevseason: | 1967–68 |
| Nextseason: | 1969–70 |
The 1968–69 Alpha Ethniki was the 33rd season of the highest football league of Greece. The season began on 22 September 1968 and ended on 15 June 1969. Panathinaikos won their ninth Greek title and their first one in three years.
The point system was: Win: 3 points - Draw: 2 points - Loss: 1 point.
|+Relegation play-offs|}
| Rank | Player | Club | Goals | |
|---|---|---|---|---|
| 1 | Giorgos Sideris | Olympiacos | 35 | |
| 2 | Georgios Dedes | Panionios | 25 | |
| 3 | Giorgos Koudas | PAOK | 20 | |
| Mimis Papaioannou | AEK Athens | |||
| 5 | Giorgos Gonios | Panathinaikos | 18 | |
| 6 | Thanasis Intzoglou | Panionios | 17 | |
| Sakis Kouvas | Vyzas | |||
| 8 | Vasilis Kyriakou | Apollon Athens | 14 | |
| Alekos Alexiadis | Aris | |||
| 10 | Michalis Kritikopoulos | Ethnikos Piraeus | 13 |