St. Mary’s Church in Tartu was built in 1842 to be the home church of the city of Tartu and the Estonians in the parish. Prominent parish members included, for example, M. Härma, L. Koidula, and J. V. Jannsen. In 1869, the first Estonian song festival was initiated in St. Mary's Church in Tartu, which is why the church is also called the cradle of the song festival.
The church was destroyed on July 12, 1941 and was reconstructed as a gym for the Estonian Academy of Agriculture. The church remained as a sanctuary for sports in Tartu for almost 50 years.

The church was returned to the parish again in 2009 and is presently being restored. In 2022 the restoration works of the tower, which had been demolished while turning the church into a gym, were finished. A golden rooster stands guard on the tower.