Saint Anne's Church in Warsaw was built in 1454 near the monastery of the Bernardine Order, founded by Duchess Anna of Masovia, who in 1454 brought from Krakow the first Franciscans more strictly adhering to the rules, who had settled there a year earlier, and in Poland they were called Bernardines.The church was constructed in the Gothic style and consecrated on December 4, 1454, by Bishop Andrzej Bninśki of Poznań. In 1507, both the church and monastery were destroyed in a fire. They were restored through the efforts of Guardian Antoni from Bech and Jan from Komorów, but in 1515, they once again burned down in another fire. In 1533, the temple was restored with the funds provided by Anna Radziwiłł, Beata Temchinska, and Jan Lubrański, the Bishop of Poznań.
During the Swedish invasion, the church was not destroyed but was converted into a fortress by the Protestants. The temple suffered during the siege of Warsaw by the army of Transylvanian Prince George II Rákóczi in 1657.
In 1660, the monastery was reestablished with the participation of Castellan Jan Wielkopolski the Elder. In 1663, the restoration of the church began, according to the design of architects Giovanni Battista Gisleni and Tylman van Gameren, which was completed in 1670. An organ made by Antoni of Glogów and Klemens of Serpukhov was installed in the church. In 1676, the Warsaw General Seminary, or the Bernardine Seminary, was opened at the monastery, receiving the status of a first-class educational institution—the highest degree for an educational institution in the kingdom. In 1701, a garden was arranged at the monastery.
In the mid-18th century, the facade of the church was reconstructed in the Rococo style according to the design of architect Jakub Fontana, adorned with two filigree bell towers. The interior of the church was decorated with paintings by monk Walenty Jeżewski depicting scenes from the "Life of Saint Anne". From 1786 to 1788, Stanisław Kostka Potocki, with the participation of King Stanisław August Poniatowski and citizen Józef Kwecinski, raised funds for the reconstruction of the church's facade, which was restored in the neoclassical style by architect Piotr Aigner. During that time, the Chapel of the Sokalska Bogomater was also established in the church with funds provided by Józef Kwecinski.
During the Warsaw Uprising of 1794, the insurgents hanged Bishop Józef Kossakowski in the square in front of the church, accusing him of treason in favor of Russia. After the establishment of the Kingdom of Poland within the Russian Empire, the monastery effectively ceased to exist.
The church did not suffer significant damage during the bombing of Warsaw in 1939 at the beginning of World War II, however, the temple burned down during the Warsaw Uprising in 1944, but it was completely restored during the reconstruction from 1946 to 1962.
The church is located in close proximity to four major higher education institutions in Warsaw—the University of Warsaw, the Academy of Fine Arts, the Frederic Chopin University of Music, and the Theatre Academy. For this reason, since 1928, its custodian has served as the university chaplain.
On June 3, 1979, Pope John Paul II made his first pilgrimage to his homeland and met with Polish youth at this church. In memory of this event, a memorial plaque is installed at the entrance of the church.
Having been restored several times throughout its history, the temple is a mix of various architectural styles - late Gothic (altar), high Baroque, Classicism, and Neo-Renaissance (bell tower).
The Classicist facade of the temple is adorned with sculptures of the four evangelists by Jakub Monaldi and Franciszek Pinck. The church's interior is in the style of high Baroque. There are several chapels in the temple. In the Loreto Chapel, there are burial places. The walls and ceiling are decorated with frescoes.
In Saint Anne's Church, there is the only crystal vault in Warsaw, which can be seen in the monastery on the way to the vestry. It was created in 1514 by the architect Jan of Komorowo.