| Estonian Championship | |
| Year: | 1939–40 |
| Defending Champions: | Estonia Tallinn |
| Winners: | Olümpia Tallinn (1st title) |
| Prev Season: | 1938–39 |
| Next Season: | 1941 |
The 1939–40 Estonian Football Championship was the 19th official top-division football league season in Estonia, organized by the Estonian Football Association. It was the last season before World War II. PK Olümpia Tartu won the title.
| Pos | Name | Team | Goals |
|---|---|---|---|
| 1 | Nikolai Linberg | JS Estonia Tallinn | 15 |
| 2 | Richard Kuremaa | PK Olümpia Tartu | 13 |
| 3 | Boriss Riisik | PK Olümpia Tartu | 9 |
| 4 | Arnold Truks | ÜENÜTO | 8 |
| Hugo Ööbik | VS Sport Tallinn | 8 | |
| 6 | Albert Leichner | Tallinna Jalgpalliklubi | 7 |
| Richard Kägu | Tallinna Jalgpalliklubi | 7 | |
| Artur Kald | SÜ Esta Tallinn | 7 |