The team first competed internationally in the 1936 Summer Olympics, finishing in 9th place. Estonia has made 5 appearances at the EuroBasket with best results coming from 1937 and 1939, when the team finished in 5th place.
Estonia competed in the 1936 Summer Olympics, held in Berlin, Germany, the first Olympic tournament to hold basketball as an official medal event. Coached by Herbert Niiler, the team played and won against France in the first Olympic basketball tournament game ever but lost to the United States in the second round and to the Philippines in the third round, leaving Estonia in 9th place.
Estonia participated in the EuroBasket 1937. The team won their first match against Egypt but failed to advance past the group stage after suffering defeats to Lithuania and Italy. Estonia placed 5th in the final rankings after defeating Czechoslovakia and Latvia. The EuroBasket 1939 used a different format from the previous championship, with 8 teams facing off in a round-robin tournament. Estonia finished the tournament with a 4–3 record and another 5th place. Heino Veskila was the scoring leader with 16.7 points per game.
Estonia participated in the FIBA EuroBasket 2001, held in Turkey. Estonia lost all three preliminary round matches, despite Martin Müürsepp leading the team with 18.3 points per game and finished the championship with a 0–3 record and a disappointing 14th place. Margus Metstak was the team's rebounding leader with 6.0 rebounds per game, while Rauno Pehka and Tanel Tein averaged 2.7 assists per game. After 2001, Estonia failed to qualify for another major basketball tournament for 14 years. The team competed in the FIBA EuroBasket 2011 Division B tournament, winning their group.
Estonia qualified to the FIBA EuroBasket 2015, with preliminary round matches held in Riga, Latvia. Estonia's first two performances were poor as the team suffered heavy defeats in games against Czech Republic (57–80) and Belgium (55–84). The team, however, bounced back with a 78–71 victory against Ukraine, their first EuroBasket victory since 1993. The next game saw the team defeated by Lithuania 62–64 in a close game. In the final group phase game, Estonia played against Latvia, losing 64–75 and failing to advance to the knockout stage. Estonia finished the championship in 20th place with a 1–4 record. Gregor Arbet was the team's scoring leader with 11.6 points per game, while Siim-Sander Vene averaged 6.4 rebounds and Sten Sokk contributed 4.2 assists per game.