The first church of St. Anne was built on this site in 14th century. That temple was burnt down during anti-Jewish riots and it was rebuilt with Wladyslaw Jagiello's sponsorship in 1407. The Gothic building survived until the end of the 17th century, when University decided that a new church was necessary.

The construction and decoration of the new temple took place from 1689 to 1703. The design was entrusted to the Tylman from Gameren with the suggestion to model the church on S. Andrea della Valle in Rome.

St. Anne's was raised on a Latin cross plan, with the dome resting on the nave-transept crossing. The corpus of the church was composed of a wide main nave with three pairs of side chapels. Tylman from Gameren created a monumental temple - one of Poland's most beautiful Baroque churches. The exterior of the St Anne is decorated by the light, Late Baroque crownings of the towers, raised about 1778 to a design by Father Sebastian Sierakowski. The main iconographic theme, depicted on the walls and vaults of the chancel and nave, is the Incarnation of Christ.

For centuries the church was as much a university building as the colleges and dorms. Official inaugurations of the academic year took place here, their centerpoint being the parade of robed professors to the auditorium for the opening lecture.