Jonas Zaberezinskis, Marshal of Lithuania and Trakai Voivode, owner of Alytus Manor, built the church around 1520. The parish was founded in 1524. For a time the church was attended by Catholics from both parts of the city. According to the founding charter, the pastor of the church had to speak Lithuanian. In 1658 the church was rebuilt. In 1763 a new wooden church was built. In 1773 a parish school was established. In 1810 the church burned down in a fire in the city.
In the years 1818-1820 the pastor Liudvikas Kaminskas and his parishioners built the current church. Until 1842, the village of Skraičioniai belonged to the municipality. In 1930 the church was enlarged and renovated by the pastor Konstantinas Paulavičius, appointed in 1910. A tower was added and the churchyard fence was made of stone.
On June 24, 1941, the Nazis shot and killed Pastor K. Paulavičius and Vicar Vincentas Mazurkevičius. They are buried in the churchyard; a small shrine was built. Destroyed during World War II, the church and tower were rebuilt around 1957 under the direction of Pastor Leonas Jakubauskas (translated from Wikipedia).