It was first named San Paolo, St Paul's, after an older chapel on the site. At the battle of the White Mountain at Prague in 1620, the imperial forces saved Bohemia for the Church, and their Carmelite chaplain had carried a picture of the Nativity around his neck. The image was brought to Prague, and from there to Rome. It was at first taken to Santa Maria Maggiore, and from there carried in procession to San Paolo, which was still unfinished. It was then decided to dedicate the church to the Blessed Virgin in gratitude for the victory.
It was partially destroyed by fire in 1833, and later restored.
The paintings in the vault, depicting Mary among the angels and the fall of the evil angels, are by Giovanni Domenico Cerrini. They were painted c. 1675. Cerrini also painted the angels in the cupola.
In the apse above the high altar is a painting of the Entrance of the image of the Madonna into Prague, made in the 19th century restoration.