The original buildings were destroyed in the devastating fire that swept through the ghetto in 1689. Between 1689 and 1694, a new synagogue in the early Baroque style was erected on the same site by the builder Shelomo Chaish Cohen. Shortly afterwards, in 1696, a monumental three-tiered Torah ark was added at the expense of Samuel Oppenheimer. The present Baroque building is the largest synagogue in Josefov and the only example of early Baroque architecture in the former Prague ghetto.
The synagogue held an exceptional place in the life of Prague's Jewish community. It served as the second main synagogue of the Prague Jewish congregation and as the house of prayer for the Chevra Kadisha burial brotherhood, an institution responsible for funerals, cemeteries, and the care of the sick and dying. Many prominent rabbis officiated here, among them Eleazar Fleckeles. The building stands immediately beside the Old Jewish Cemetery, with which it shares a profound historical bond.
In 1883–1884, the synagogue underwent repair and restoration to a design by the architect Bedřich Münzberger, who also contributed to the decoration of the Spanish Synagogue. During the urban clearance of Josefov at the turn of the 20th century, the synagogue was spared, unlike many other ghetto buildings that were demolished at that time. During World War II it was used as a warehouse and as part of the wartime Central Jewish Museum. Further restoration work took place in 1960, 1979–1981, and 1995–1996. Of the original 17th-century structure, only the window shapes and an inscription plaque on a pillar — dating the synagogue's founding to 1694 — have survived.
For decades the synagogue housed a permanent exhibition devoted to Jewish traditions and customs. The building is currently closed for comprehensive renovation, which is expected to be completed around 2028. Once finished, the synagogue will reopen to the public with a new permanent exhibition. Address: U Starého hřbitova 3a, Prague 1.