In the early 17th century the synagogue underwent extensive reconstruction: the builder Judah de Herz added a women's gallery, a vestibule, and an entrance hall. The building displays features of Late Gothic architecture alongside an early Renaissance portal. The main space is lit by five windows with stone tracery, while the walls are adorned with engaged pilasters and painting in imitation of Renaissance stucco. At the centre of the nave stands a stone bimah enclosed by a Rococo grille bearing the motifs of the Star of David and the Jewish hat, donated by Joachim Popper. Flanking the Torah ark (aron ha-kodesh) are inscribed the names of the ghettos and concentration camps to which transports from the Czech lands were sent.
Between 1955 and 1960 the synagogue was transformed into a Memorial to the Victims of the Shoah. At the initiative of Hana Volavková, the first post-war director of the museum, the painters Václav Boštík and Jiří John covered the walls of the entire interior with the names, dates of birth, and dates of death of nearly 80,000 Bohemian and Moravian Jews who perished during the Second World War. The result was one of the oldest and most powerful Holocaust memorials in Europe. Following the Soviet invasion of 1968, the memorial was closed by the communist authorities and the inscriptions deliberately destroyed. Restoration took decades, and the fully reconstructed synagogue was not reopened to the public until 1995.
The upper floor houses a permanent exhibition of children's drawings from the Terezín ghetto (1942–1944). This unique collection comprises 4,387 drawings created in the ghetto under the guidance of the artist Friedl Dicker-Brandeis. They depict everyday life, memories of home, and the dreams of children imprisoned behind its walls. More than ten thousand children under the age of fifteen passed through the Terezín ghetto; for many of them, these drawings are the only surviving trace. Since 2025, the collection has been inscribed in the UNESCO Memory of the World International Register.
The synagogue is located at Široká 3, Prague 1 and is included in the ticket for the Prague Jewish Quarter circuit. Those researching family history or the individual fates of Shoah victims can make use of the digital database available at pinkas.jewishmuseum.cz, which holds the names of victims alongside available digitised documents.