Like the city of Tallinn, the Jewish community of Tartu was founded mainly by retired Russian soldiers, previously stationed in the city. Thus, the former soldiers of Nicholas built a synagogue in 1876 in the city of Tartu.

By the turn of the 20th century, there were nearly 1,800 Jews in the city and thriving educational institutions. Among them is the Association for the Study of Jewish History and Literature. Among its members is Jacob Bernstein Kogan.

However, this figure declined and they were only 920 in 1934. One consequence of the Russification of the University of Tartu, which imposed a quota, reducing the number of eligible Jewish students.

A Jewish Studies Seminar was opened at the university in 1934, under the direction of L. Gulkowitsch, then M.J. Nadel and H.J. Welcoming Port. This intense intellectual life was interrupted by the Soviet invasion and then the German occupation. The Shoah claimed many lives in the city. The synagogue was destroyed during the war. The Estonian National Museum now preserves artifacts that were present there.

In the aftermath of the war, 200 Jews returned to the city, later joined by Jews from other parts of the USSR. However, many of them emigrated to Israel around the turn of the Six-Day War.