The church was built on the foundations of the Gothic Church of St. Clement, affiliated with the Dominican Order. For many years, from the turn of the 16th-17th century, it was gradually built by anonymous people, then by Carlo Lurago and Francesco Caratti. As early as 1578 - 1581, the Society of Jesus, led by Rector Giovanni Paolo Campana, laid the foundations of the building, then a chancel and a transept were built.
In 1581, the primate of the neighboring Jewish ghetto, Mordechai Maisel donated 100 thalers to build the church, which testifies to a completely unprecedented tolerant atmosphere and the peaceful coexistence of different religions within Rudolfinian Prague.[2]
At the beginning of the 17th century, a whole nave and a western marble portal with a portico were built. The church received built-in emporiums and stucco decoration. The construction was managed by the Italian architect Carlo Lurago. At the end of the 1740s, a dome was hung above the sanctuary, decorated with stucco from the workshop of Johann Georg Bendl. This is the so-called false dome of the octagonal floor plan on the tholobate. The stucco decoration later had to be removed for its weight and replaced with a new one. From 1654 to 1659, according to Lurago's design, a new representative façade was built with three arched arcades reminiscent of Roman triumphal arches. The church towers were modified and raised in 1714 by architect František Maximilián Kaňka.[3]
In the 18th century, anti-Reformation Jesuit theologian Antonín Koniáš occasionally preached in the church. Between 1805 and 1819, Bernard Bolzano, a university preacher, was here. Jakub Jan Ryba played the organ here in the 1880s.[4] In 1950, Oto Mádr devoted himself to the pastoral care of university youth.[5]
