The Karaite prayer house was first mentioned in a letter of Sigismund I dated 22 December 1506. In the first half of the 17th century the Karaite community made efforts to obtain permission from Sigismund III Vasa to construct stone prayer houses in place of the existing wooden ones.
The Rabbanite community was granted such a permission in 1626. However, the Karaites were not permitted to construct a stone building since their synagogue was situated outside the fortifications and could not contribute to the defence system of the city.
In 1633 Sigismund III's successor, Ladislaus IV acknowledged the right of the Karaites to possess a wooden prayer house. In the 18th century the building was at least twice devoured by fire.
In 1915 this historical edifice was ransacked by Austrian troops. In the paper an attempt to establish the kind of its furnishings is made based on two relations of 1821 and 1908 and an inventory list of 1883.