The Pinkas synagogue was evidently built on the location of an old 15th century synagogue, after the synagogue in the German town of Regensburg had been destroyed, many of its Jewish population slaughtered and the famous rabbi R. Shlomo Molcho arrested in Regensburg by Emperor Charles V, who turned him over to the inquisition of Mantua which burned him at the stake in 1532. Built in the late Gothic style, many design and interior details bore a resemblance to the Pinkas shul in Regensburg. All the more so since R. Molcho's tallith and kaftan were stored there. Such was R. Aharon Meshulam's response to the calamities which befell the Regensburg Jews - to build a larger and more splendid synagogue. It was not a simple task to obtain permission from the authorities to build a synagogue, but Aharon Meshulam, being one of the leaders of the Prague Jewish community, had access to the Burggrave of Prague, Lev of Rozmital and King of Bohemia, Ludvik, who earlier, in 1525, had issued an order granting various privileges to Aharon Mesulam and all his family. The latter also succeeded in finding a good architect, one of the masters of famous Rejt who built a wing of Hradchany Castle, now known as the Ludvik Palace, as well as the Lev of Rozmital's new palace at Blatna.
A man of the House of Levi has passed, and his name was Aharon Meshulam, and he ascended the stairway of the bounteous spirit, following the steps of his Fathers - Princes and Leaders - and he built this synagogue, a splendid monument. And his wife, lady Nechama, the daughter of Rabbi Menachem of blessed memory, was a helpmate and companion to him for the memory of the soul. In the year (5)295 (of the Jewish calendar, i.e. 1535) he began the work, and it was finished in honor of G-d, may He reign supreme, and in honor of the Torah. Here is the holy community of Prague crowned. The eyes of G-d are on it, it is remembered and guarded. - Aharon Meshulam, a son of Rabbi Yishayahu Ha-Levi of blessed memory, called Zalman Horowitz.
Though the family synagogue of the Horowitzes, it served not only them: among the names of the congregation's members in various periods one can find R. Shlomo Ephraim ben Aharon of Leczyca, the author of "Keli Yaqar", MaHaRaL of Prague, R. Israel ben Kalman Brandeis, R. Yakov ben Yona Teumim, and others.
During the German occupation of World War II the Nazis planned to make the synagogue and the adjacent Old Jewish Cemetery part of a postwar "Exotic Museum of an Extinct Race". After the war it was repaired and restored, and now it is one of the pearls of the Old Jewish Quarter in Prague. The names of 77,297 Czech Jews who perished in the Holocaust have been inscribed on its walls.