The St Agnes Convent was founded by the Premyslid Princess Anezka (Agnes), sister of King Vaclav I in 1231 as the first convent of the Order of Poor Clares north of the Alps. It was the first Gothic building in Prague. The grounds originally had a larger Poor Clare convent and less significant monastery of smaller brothers that was later closed. In its time the convent was an influential spiritual centre in the history of our nation, and was also the Premyslid burial-grounds. However, after the death of its founder, the great era of the convent ended and its importance waned. Shortly after the mid 16th century the Poor Clares were evicted and the building fell into the hands of the Dominicans for roughly seventy years. The Poor Clares were then forcibly returned to the dilapidated convent, but only partial Baroque renovations were made to the devastated building. The convent was one of the firsts to be closed.

It was shut down in January 1782 and thereafter used as workshops, storage facilities and homes for the indigent. Before its demolition as part of the "Old Town Slum Clearance" it was saved through the efforts of the Union for the Renewal of the Convent of the Blessed Agnes. It was renovated in 1963 to meet the exhibition needs of the National Gallery. The convent building was newly opened in year 2006 after the complete reconstruction /destroyed by floods in 2002/.