The synagogue building was constructed in 1867 in the Kingdom of Croatia-Slavonia within the Austrian Empire, and was used until it was demolished by the Ustaše fascist authorities in 1941 in the Axis-aligned Independent State of Croatia.

Major disagreements exist between the government and Jewish organizations as to how much the latter should be involved in decisions about the reconstruction project, including proposed design and character of the new building.

Encouraged by the 1782 Edict of Tolerance of Emperor Joseph II, Jews first permanently settled in Zagreb in the late eighteenth century, and founded the Jewish community in 1806.

[2] Klein, a representative of romantic historicism, modeled the building on the Viennese Leopoldstädter Tempel (1858), a Moorish Revival temple designed by Ludwig Förster.

[2] The composition of the main facade, with its dominant drawn-out and elevated projection and the two symmetrical lower lateral parts, reflects the internal division into three naves.

[2] The synagogue was officially consecrated on September 27, 1867, a ceremony attended by representatives of city and regional authorities, Zagreb public figures, and many citizens.

[12] The small minority of Orthodox Jews found this change to be intolerable, and they began to hold their services separately, in rented rooms.

The Ustaša quickly started with the systematic persecution of the Jews, modeled after the Nazi Germany approach, and at times even more brutal.

[15] Racial laws were introduced, Jewish property was confiscated, and the Jews were subjected to mass arrests and deportations to death camps in Croatia and abroad.

[15] In October 1941, the newly installed mayor of Zagreb, Ivan Werner, issued a decree ordering the demolition of the Praška Street synagogue, ostensibly because it did not fit into the city's master plan.

[18] The synagogue's eight valuable Torah scrolls were saved due to an intervention by Leonardo Grivičić, an entrepreneur and industrialist who lived next door from Mile Budak, a minister in the Ustaša government.

[19] By that evening, Grivičić secretly relayed the information to the synagogue's chief cantor, Grüner, and during the night, the Torah scrolls were moved to safety.

[19] Shortly after the destruction of the synagogue, the Catholic archbishop of Zagreb Aloysius Stepinac delivered a homily in which he said: "A house of God of any faith is a holy thing, and whoever harms it will pay with their lives.

[4][22] The Yugoslav communist regime nationalized virtually all real estate owned by the Jewish Community of Zagreb, including the plot in Praška Street.

[16] Two architects, Branko Silađin and Boris Morsan, both of whom participated in the failed 1977 department store competition, came forward on their own accord and contributed their ideas for a new Jewish center in Praška Street.

[16] Silađin's vision was ultimately not accepted by the Jewish community; instead, plans were being made for the construction of the cultural center and a synagogue, following an international architecture competition.

Bienenfeld declined the offer believing to be inappropriate when a great number of churches are left destroyed at the time, during Croatian War of Independence.

[31] In a 2021 interview, Ognjen Kraus confirmed there were plans for rebuilding the synagogue, but expressed frustration with lack of engagement from the city and government, especially after the 2020 Zagreb earthquake.