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The first wooden church was built in 1604. It was a branch of Birštonas parish. Bishop Benediktas Vaina converted Birštonas church into a branch of Prienai parish. In 1609, Prienai Church was gifted the Bagrėnas farmstead with buildings, as well as the Bagrėnas village with 33 voloks of land. The pastor was obliged to support the vicar. The pastor also had to be Lithuanian or speak the Lithuanian language fluently. The church had a parish school at the beginning of the 17th century. Metrics books were written in the church as of 1644. A new church was built in 1674 under the care of pastor Vaitiekus Izdebskis.
The current wooded church was built in 1750. It was repaired and expanded in 1875. At the time, a brick chapel was built in the churchyard. The new church was consecrated in 1885 by bishop Juozapas Olekas. A library – reading room was established here in 1907. An organ made by a famous Lithuanian artist Jonas Garalevičius was installed in the church. In 1918, "Žiburio" gymnasium was founded whose long-time director was priest Feliksas Martišius (1879–1955).
The church was repaired after World War II. Prienai vicar - priest Juozas Zdebskis was arrested on 26 August 1971 and sentenced to serve 1 year in Pravieniškės prison for the catechization of children.
The church was repaired in 2017 and repainted to its original green colour.
The two-tower, cross-plan church has features of Neo-Baroque architecture, a three-sided apse and 4 small towers. The churchyard is surrounded by a brick fence.