The Jewish congregation in Copenhagen purchased a 900 square metre site outside the city for use as a burial site in the early 1690s. The oldest burial in the cemetery is from 1694. Further acquisitions of land had brought the cemetery up to its current size by 1854 but it was still passed out of use when a new Jewish cemetery opened in connection with the new Vestre Cemetery.
The brick wall which today surrounds the cemetery on three sides, along Møllegade, Guldbergsgade and Birkegade, was built in 1873 to a design by Vilhelm Tvede. The entrance is on Møllegade. The cemetery was listed in 1983.