The church along with a monastery of the Carmelite order was founded in 1347 on the occasion of the coronation of Emperor Charles IV and his wife Blanche of Valois.
Emperor Charles then donated a large plot to them which they could partly rent out for income, along with the wood which had been used to build his coronation hall.
During the Hussite Wars of the 15th century, construction was interrupted, the church was heavily damaged, and the friars abandoned the monastery.
At the beginning of the 17th century the church was taken over by the Friars Minor, to whom it was entrusted by the King of Bohemia Emperor Rudolf II.
In 1611, during the Passau army incursion, the community of fourteen friars were killed when a Lutheran rabble from the city of Prague attacked and looted the monastery.
The northern aisle is accessible from the eastern corner of Jungmann Square through the gate which originally led to the cemetery behind the church.
According to the last archaeological research from the 1980s and preserved contemporary documentation, the church was meant to be about 110 meters long.
The builders decided to make the chancel taller, which resulted in enlarging of the buttress system.
Over the entrance to the aisle is a tympanum with the relief picturing God the Father, Jesus Christ and Holy Spirit.
The original Gothic vault, which was even higher than the current one, was already completely destroyed by the end of the 16th century.