| Competition: | Panhellenic Championship |
| Season: | 1939–40 |
| Winners: | AEK Athens 2nd Greek title |
| Relegated: | none |
| League Topscorer: | Kleanthis Maropoulos (2 goals) |
| Biggest Home Win: | AEK Athens 1–0 PAOK |
| Biggest Away Win: | PAOK 3–4 AEK Athens |
| Highest Scoring: | PAOK 3–4 AEK Athens |
| Matches: | 2 |
| Total Goals: | 8 |
| Longest Wins: | AEK Athens (2 matches) |
| Longest Unbeaten: | AEK Athens (2 matches) |
| Longest Winless: | PAOK (2 matches) |
| Longest Losses: | PAOK (2 matches) |
| Highest Attendance: | 3,000 |
| Prevseason: | 1938–39 |
| Nextseason: | 1940–41 |
The 1939–40 Panhellenic Championship was the 11th season of the highest football league of Greece and the last before the WW2 took place. It was carried out with a system similar to that of the previous season in which 14 teams participated again, 8 from the Central and 6 from North Greece, which were divided into groups. As in the previous year, in order to complete the championship, since it took a total of 30 matchdays, the teams that qualified for the national championship did not compete with each other again but transferred the mutual results of the local championships.
The teams of the Central Greece formed the South group and resulted as follows:
The teams of the Νorth Group were initially divided into two subgroups. The teams of the Thessaloniki formed the North subgroup A and resulted as follows:
The teams of Serres, East Macedonia and Thrace formed the North subgroup B and resulted as follows:
The two winners competed in double games to become the champion of the Northe group. The champions of South and North, AEK Athens and PAOK, competed in a 2-legged final for the title. AEK was crowned champion for their 2nd Championship (2 consecutive), with Kleanthis Maropoulos being the protagonist as the last year. AEK had a great team then and throughout the year they had only one defeat in the South group against Olympiacos. Both in the local championship of Athens, and in both of the finals, AEK achieved only victories. The point system was: Win: 3 points - Draw: 2 points - Loss: 1 point.
| width=190 | Team | width=28 | width=28 | width=28 | width=28 | width=28 | Qualification | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Olympiacos (Q) | 10 | 49 | 10 | +39 | 28 | South Group | ||||||
| 2 | Ethnikos Piraeus (Q) | 10 | 21 | 8 | +13 | 26 | |||||||
| 3 | Proodeftiki (Q) | 10 | 23 | 19 | +4 | 23 | |||||||
| 4 | Thiseus Piraeus | 10 | 8 | 18 | -10 | 15 | |||||||
| 5 | Argonaftis Piraeus | 10 | 12 | 26 | -14 | 14 | |||||||
| 6 | Aris Piraeus | 10 | 9 | 29 | -20 | 13 | |||||||
a. The ranking and the points are the final but the reported goal difference is of the 7th matchday.
b. The ranking and the points are the final but the reported goal difference is of the penultimate (9th) matchday.
|}
|+Summary|}
AEK Athens won 5–3 on aggregate.
| Rank | Player | Club | Goals |
|---|---|---|---|
| 1 | Kleanthis Maropoulos | AEK Athens | 2 |
| 2 |  Kostas Vasiliou | AEK Athens | 1 |
| Alekos Chatzistavridis | AEK Athens | ||
| Giorgos Gasparis | AEK Athens | ||
| Kostas Kalogiannis | PAOK | ||
| Feroutsos | PAOK | ||
| Aristidιs Ioannidis | PAOK |