The City of Kaunas was chosen as its site, since the historic capital of Lithuania, Vilnius, was part of Poland between 1920 and 1939.

A design competition was held in 1928 and the proposal drawn up by Karolis Reisonas was chosen for the church as the best.

The prominent Lithuanian parson Feliksas Kapočius was particularly involved not only in the details of the building project, but also in its funding.

In 1938 the walls and roof of the church were completed, and by 1940 it was largely finished; at this point around one million litas had been spent, most of it from individual donations.

During the 1990s, its rehabilitation met with further obstacles; church and state had been officially separated, and Lithuanian citizens struggled with economic downturns during the transition to a market economy.

The church is not solely dedicated to Roman Catholic ceremonies - it is also used for community gatherings and events, and as a preschool.