[1][2] The Church of the Assumption of the Virgin Mary is the oldest Gothic building in Kaunas, though the foundation documents for the structure are not known to exist (they have either been misplaced or destroyed).

According to the Jesuit historian Albertas Kojelavičius-Vijūkas, the church was constructed under the auspices of Vytautas the Great in 1400 as a commendation to the Blessed Virgin Mary for saving his life after a major defeat in the Battle of the Vorskla River, and was subsequently overseen by Franciscan friars invited from Vilnius.

[3] During the major fires that afflicted Kaunas in 1603, 1624 and 1668, the church, situated away from the conflagrations and on the banks of the Nemunas river, was likely to have sustained minimal damage when compared with other structures in the city.

In 1819, the church underwent further restoration, initiated by the Franciscan Abbot, Grigalius Golickis, which included the construction of new vaults and the paving of the floor with bricks.

After the Commonwealth was partitioned, the Grand Duchy of Lithuania came under Russian rule, and as part of a rigorous policy of consolidating Orthodoxy and Russification, the church was closed in 1845 and the monastery was abolished.

Over the years the ground level around the church has been raised significantly and the façades became lower; to compensate for this, the windows were shortened and the side portals were removed.