The Piarist order was brought to Litomysl by Frebonie of Pernštejn in 1640. The Piarists (who came to Litomysl from Mikulov) were an order of pedagogues, whose aim was to educate poor children in their schools. The Piarist grammar school in Litomysl was opened in 1644. At that time three wings of the Piarist college (the last was built in 1681), the school and a small church all stood on the site of today's church. Part of the college was a refectory with stucco and painted decorations and a similarly decorated chapel known as Purgatory. When the college was built, a large, later to be altered on several occasions, garden and orchard was also established, which today forms an important part of the complex known as the Monastery Gardens
In 1714 the owner of the Litomysl demesne, Count Franz Wenzel von Trautmannsdorf, began to build a large new church and new schools. In place of the original plans by Nicola Rossi the project as taken over by the famous baroque architect Giovanni Battista Alliprandi (who is also buried in the Provost church in Litomysl). Following his death in 1720, the work was completed by František Maxmilián Kaòka, who designed both the façade and the interior. The school (today's museum and gallery) was completed in 1719 (a statue of the founder of the order - St. Josef Kalasanský - was placed above the portal), and the church was completed three years later. A number of other famous artists contributed to the decoration of the church - the statues of the four evangelists and Sts. Wenceslas and Prokop were made by the workshop of M. B. Braun, the vaulting of the dome was painted in 1728 by Václav Jindøich Nosek and the picture at the main altar was the renowned Italian artist F. Trevisani. The church became an integral part of the panorama of the city, and is one of the most important baroque buildings in the region.
The church has suffered several fires - especially those in 1735, 1775 and 1814. During the fire of 1775 the interior fittings were severely damaged, as were the paintings inside the dome, which were not renewed, and the altar picture was destroyed; this was replaced three years later by a copy by a professor from the Vienna Academy, V. Fischer. More fittings were added during the 19th century.
The organ, once one of the best instruments in Eastern Bohemia, today unfortunately in a derelict state, was built in the 1820's by the Kutná Hora organ builder, Horák.
The church was used in particular for services for the Piarist monks and students at their schools. It also became the final resting place of members of the order and Counts from the Trautmannsdorf and Wallenstein-Warttemberg families.
The Piarists left Litomysl in 1948. In 1948-1949 the last renovation of the church took place (renovation of the tower and roof).
As early as 1958, when it was first officially recognised that the church was in a derelict state, unsuccessful attempts were made to reconstruct the building. In 1972 the church was passed into state ownership (since when it has been managed by the Pardubice Monument Office, formerly known as KSSPPOP). In 1978 a project was drawn up for its overall reconstruction, but work on this never started. In 1981-82 the interior fittings of the church were removed and part of the furniture was sent for restoration. The planned removal of the statues of the Evangelists and the organ did not however take place and the work was postponed once again. At the beginning of the 1990's several concerts were held in the church as part of the Smetana's Litomysl festival.
In 1967 it was discovered that the tombs in the crypt of the church had been demolished, and vandals had played their part in the destruction of other parts of the building.
A partial reconstruction of the church took place from 1991-1994. The roof was repaired (especially the dangerous condition of the timberwork), as were both towers and the façade. From 1997-2000 the college buildings were repaired. The Piarist church is not open to the public at present, and the restoration of the interior of this important monument is still awaited.