Franciscans were already present in Vilnius around the middle of the 13th century, long before Lithuania was baptised (1387). In 1323, i.e. at the time of Lithuanian Duke Gediminas (Gediminas, c. 1275-1341), the monks had a small brick temple located somewhere in the area of the Lower Castle and the Cathedral.

Today's Franciscan temple was located on the edge of what was then Vilnius, in its south-western part, by the road leading to Trakai and then to Poland. This was an area inhabited by settlers from Western Europe, mainly German-speaking, for whom a modest brick church of St Nicholas had already been built (before 1387).

The spacious Franciscan church was built as a parish church with the foundation of King Vladislovas Jogaila, Lithuanian Grand Duke Vytautas and Hanul of Riga, who was the starosta of Vilnius. The date of its consecration is sometimes given as 1421, but this is uncertain. It is assumed that the block stood until around 1430. The temple was built as a towerless, three-nave hall with buttresses extending outwards. There were originally two cylindrical staircases on the side of the façade (the northern one is preserved). The façades of the church were enlivened by geometric ornamentation, arranged in ixes and rhombuses, drawn out in dark brick. The architecture of the church was therefore in keeping with the architecture of the Baltic lowlands, where its creators came from. As it was a mendican church and the monks were obliged to pray in communion, the body of the church is adjoined by a long choir closed with a trilateral console. Probably still in the 15th century, a chapel dedicated to Mary was added to the north side of the church. After a fire in the church in 1530, thatchers from the same Baltic region built two chapels adjoining the choir to the south, which are covered by picturesque and chiaroscuro crystal vaults.

Originally, the top of the church was stepped, as it is visible on the oldest views of Vilnius. It was rebuilt in 1778, just like the walls of the church, introducing the basilica scheme, i.e. with a higher nave. The ogival windows of the side aisles and the façade were also changed at that time. At the same time, the Gothic portal of profiled brick, built in the first half of the 15th century, was covered with pilasters and cornices. The modernisation work was carried out by the renowned Vilnius architect Augustyn Kossakowski and the Franciscan Kazimierz Kamieński, who studied architecture in Padua. A little earlier, in the mid-18th century, a domed chapel of the Oginskis was built on the northern side of the choir, as their family mausoleum.

The church and monastery were closed down in 1949 by the Soviet authorities, with the church being used as an archive for the NKVD. In 1998, the church was returned to the Franciscans in a deplorable condition. The temple has become beautiful again in recent years, thanks to the financial contribution of the Polish National Foundation, which paid for the reconstruction of the organ and is now supporting the conservation of the paintings. The paintings were created by František Niemirowski after 1780, and tell the story of the life of St Francis by adding emblems (symbolic word-pictures) in accordance with the fashion of the time in Vilnius.