The synagogue was designed by the architectural firm Hönigsberg & Deutsch and built in 1875, along with a Jewish school.

The organ and some other items from the synagogue were saved and are now preserved at the Koprivnica Museum.

The Jewish community of Koprivnica was devastated during the war, with most of its members perishing in the Holocaust.

After the war, under the communist regime of SFR Yugoslavia, the synagogue was used as a tailoring factory and warehouse.

In 2011, restoration of the Koprivnica Synagogue began and it was listed as a cultural monument.