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A wooden church was built in 1430 on 6 voloks of land by Samogitian bishop Mikalojus Dziežgevičius. It was renewed in 1522 by King Žygimantas II (Sigismund II). The first chronicler of Lithuanian history and historian Motiejus Strijkovskis lived and served as a priest in the current Jurbarkas Church of the Holy Trinity.


Queen Bona obliged a local resident Jonas Kuncevičius to build a new church. In 1555, she gifted the village of Straižiai with 6 voloks of land to support the vicar, servants of the church and the school. The school was founded in 1557 by parson Martynas Hermanavičius. The church was rebuilt in 1655, as well as in 1741 after a fire. Sobriety was encouraged by parson Leonas Kirvelis in the middle of the 19th century.


The current brick church was built in 1901–1907 under the initiative of parson Kazimieras Marcinkevičius and vicar Antanas Kiznis. In 1907, it was consecrated by bishop Mečislovas Paliulionis. A bell gifted by American Lithuanians from Jurbarkas was added to the tower. At the end of the 19th century – 1914, Jurbarkas was known for its church choir. In 1909–1914, there was a division of the Lithuanian Catholic Temperance Society. Parson K. Marcinkevičius zealously distributed forbidden Lithuanian press. Priest A. Kiznis was an eloquent preacher. Priest Pranciškus Stakauskas established "Saulės" progymnasium in 1918.


The roof of the church, the peaks of its towers and its interior burned down during a fire that broke out in the town in 1940. After a year, the church was covered and its interior was repaired and painted. Repair works were managed by parson Anatolijus Stanevičius. The lower towers of the building were also restored later on. Under the initiative of parsons Mykolas Buožius (1911–1991; buried in the churchyard) and Antanas Slavinskas, architect K. Domanskis and constructor A. Dereškevičius designed 21 m long peaks of the towers which were lifted and fixed onto the towers on 11 August 1992.


The church has a neo-Gothic style, a cross plan and two towers. The churchyard includes the cemetery of priests who served in Jurbarkas parish, as well as a bell tower with a no longer used old church bell, and a statue of the Good Shepherd. In the summer of 1976, the statue was damaged and the graves of 4 priests were desecrated.