Present at the establishment of the Jewish Museum in Prague in 1906 were the historian Dr. Hugo Lieben and Dr. Augustin Stein, the representative of the Czech Jewish movement and later head of the Prague Jewish Community. The original aim was to preserve valuable artifacts from the Prague synagogues that had been demolished during the reconstruction of the Jewish Town at the beginning of the 20th century. The Museum was closed to the public after the Nazi occupation of Bohemia and Moravia on 15 March 1939. In 1942 the Nazis established the Central Jewish Museum, to which were shipped artifacts from all the liquidated Jewish communities and synagogues of Bohemia and Moravia. Its founding was proposed by Dr. Stein who, in co-operation with other specialist members of staff, sought to save the Jewish objects that were being confiscated by the Nazis. Following long negotiations, the Nazis approved the project to set up a central museum, albeit guided by different motives than the Museum´s founders.
After World War II, the Jewish Museum came under the administration of the Council of Jewish Communities in Czechoslovakia. In 1950, ownership was transferred to the State, which, as of 1948, was in the hands of the communists. As a result, the Museum was markedly restricted in its preservation, exhibition and educational activities. The collapse of the communist regime in 1989 created the necessary conditions that led to a change in the Museum´s status. On October 1, 1994, the Museum buildings and collections were returned to the Jewish Community of Prague and the Federation of Jewish Communities in the Czech Republic respectively. At the same time, the Jewish Museum took on new life as a non-state organization