An archaeological excavation showed that in 15th century in the area of present Pinkas Synagogue there were wells, a mikveh and inhabited houses.

The architectural plan of the annex was designed by Juda Coref de Herz (also the architect of the Maisel Synagogue).

About the same time (in 1793) successful businessman and communal leader Joachim von Popper[4]: 405–406  donated the synagogue with a wrought-iron Rococo grille which adorns the bimah.

In 1860, a radical step was taken to solve the problem of floods – the floor level of the synagogue was raised by 1,5 m. The Baroque bimah disappeared, the arrangement of the seats was modernized (seats surrounding the walls as in Old-New Synagogue were replaced by the church-like rows) and pseudo-Romanesque style dominated the space.

[5]: 60  When the Jewish Central Museum was established in the second half of 1942, the synagogue was also to serve as a repository of monuments, which it collected from Czech and Moravian communities, but also as a conservation office.

[5]: 85–90 In following five years, the walls of the synagogue were covered with names of 77,297 [6] Bohemian and Moravian Jewish victims of the Shoah.

She encouraged children to express themselves in drawing, to grapple with their grim experiences from the ghetto, as well as to capture their memories from home and dreams about the future.

Projection of photographs of Shoah victims in the form of video mapping onto the mikveh of the synagogue is freely visible every evening except Fridays and Jewish holidays from Široká Street.