The original building was extraordinary for its time: a three-aisled Renaissance temple resting on twenty pillars, it became the largest and most magnificent synagogue in the ghetto. Its builders were Judah Coref Herz and Josef Wahl. During the devastating ghetto fire of 1689 the vault collapsed and the building was shortened by a third; to this day it is supported by fourteen pillars. The synagogue underwent further alterations in the first half of the 19th century and acquired its current Neo-Gothic appearance during a reconstruction carried out at the turn of the 20th century to designs by the architect Alfred Grotte.
Mordecai Maisel was an exceptional figure in Rudolphine Prague. As a successful merchant and banker whose clients included noblemen and the imperial court, he was granted the title of court Jew by Rudolf II and served on the council of elders for many years. He was a generous patron: in addition to the synagogue, he funded the Jewish Town Hall, a hospital, and three study houses to which he summoned the celebrated Rabbi Loew, and at his own expense had the streets of the ghetto paved. Maisel died childless and, although the Emperor himself attended his funeral, shortly afterwards ordered the confiscation of his entire estate. The name of this benefactor lives on in a street at the heart of Josefov and in the synagogue itself.
During the Nazi occupation the synagogue served as a warehouse for confiscated Jewish property. After the war it was taken over by the Jewish Museum in Prague and became part of its exhibition circuit. Today it houses the permanent exhibition Jews in the Bohemian Lands from the 10th to the 18th Century, tracing the history of Jewish settlement in Bohemia and Moravia from the Middle Ages to the Enlightenment. Among the unique items on display are a ring with a Hebrew inscription dating from the 12th–13th century, a Torah curtain donated by Maisel himself, original manuscripts by Rabbi Loew, and the funeral shroud of the 16th-century Portuguese mystic Solomon Molcho. The synagogue is located at Maiselova 10, Prague 1.