In the 15th century, a small settlement started to establish itself around the Kruonis' manor of the Grand Duke of Lithuania.

Current Catholic church is located in the building which was built as a Uniate church in 1626 by the colonel of the Grand Duchy of Lithuania, distinguished in the battles with the Muscovy, Cossacks and Livonia, subcamerarius of Trakai Teodoras Bohdanas Oginskis (1568–1640).

[3] In the beginning of the 17th century, the palatial Renaissance manor was built, but did not survive up to this day, except some ruins – it was badly damaged in 1812 during Napoleonic Wars.

The Catholic church was closed in 1866 and demolished by Russian authority as a reaction to January Uprising.

[5][6] After the Soviet occupation in the surroundings of Kruonis Lithuanian partisans of The Great Fight (Didžiosios Kovos) military district were active.