A Jewish religious community was established in Český Krumlov in 1893, and in 1909 the construction of a new synagogue was started. The plans were drafted by the Prague architect Viktor Kafka, and the construction, finished in 1910, was carried out by the firm of F. Sosna. The new synagogue, constructed in the sober Neo-Romanesque style, could hold a congregation of 180 people, and its premises included a winter prayer room, classroom and an office with a flat for the rabbi.

In the second half of the 20th century, the building was not used for its original purpose and it dilapidated gradually. In 1999, the Prague Jewish Community, in collaboration with the Egon Schiele Art Centre, started a renovation of the synagogue, and both these institutions will use the building to organise exhibitions about Jewish history and to present modern plastic arts.