The Augustinian monastery was founded by King Wenceslas II in 1285. The monastery buildings were built together with St. Thomas church in 1285-1379. In the adjacent area belonging to the monastery burgher houses were built, forming the St. Thomas jurisdiction. The Gothic monastery buildings that were reduced to ashes several times, were rebuilt by Domenico de Bossi between 1694 and 1634. They were adapted to their present appearance in the late 17th century by Jan de Capauli. The church, as a part of the Augustinian monastery, was built in the place of the former early Gothic St. Thomas church and St. Dorothea chapel belonging to the Brevnov Monastery. Their remnants have been preserved in the walls of the present presbytery.

A Gothic basilica preserved under the baroque adaptations was built in two stages, in 1285-1316 and then just before 1379. In the late 16th century and early 17th century the church was repaired and partly rebuilt in the renaissance style by B. de Alberto, O.Avostalis and J. Campion de Bossi. The main renaissance porch dates back to these times (1617). During the reign of the Emperor Rudolf II at the turn of the 17th century, the church became a court church and cemetery for important persons. The present high baroque appearance of the church building with its massive front and dome is the result of its rebuilding between 1727 and 1731 designed by K.I. Dienzenhofer. Inside the church, there are ceiling frescos by V.V.Reiner, statues by F.M.Brokoff, paintings by P.P. Rubens and works of other important artists.