Prince Vratislav I founded a church in the eastern part of Prague Castle in 921.

The building was first consecrated in 925, when Prince Václav laid his grandmother Ludmila to rest. In 974-976 the sister of Prince Boleslav II undertook a diplomatic mission to Rome, and won consent to the establishment of an archbishopric and the first Benedictine convent for women in Bohemia, which she later ran as abbess. In 1142 the convent burned down for the first time. During the period of the last Premyslids the convent thrived. It was again badly damaged in the great Prague Castle fire of 1541. After it was repaired, part of the convent served for some time as a castle armoury, and a new eastern wing was built for the Benedictines. The convent was further expanded in the mid 17th century. The architect F. Caratti remodelled the basilica facade in the Baroque style. In 1782 the convent was closed, and an artillery barracks was established. The right of the princess-abbess to crown the Czech queen passed to the superior of the Foundation for Noble Ladies. In 1826 the Institute for Re-education of the Clergy was established. In the 19th century the building's abbey was razed and a new chapter deanery was constructed in its place. Since the 19th century repairs and archaeological research of the entire grounds have been ongoing. The National Gallery collections have been housed in the building since 1963.