In 1647 the city of Eisenstadt was under the rule of the princely house of Esterhazy, which had a great impact on the city and led to positive changes. In 1648, by decree of Emperor Ferdinand III Eisenstadt became a free city, Taxed paid in the amount of 16,000 guilders and 3,000 barrels of wine. In 1670 Paul I allowed to settle in Eisenstadt and six nearby settlements 3,000 Jews who were expelled from Vienna. Rabbi of the city was Vertaymer Samson, who himself was buried in the old Jewish cemetery.

There was a need in the cemetery. So there was the old Jewish cemetery in the 17th century near the Jewish Quarter. Old cemetery functioned from 1679 to 1875 years, and has about 1,140 tombstones with only Hebrew inscriptions. Because of limited space, next to the old cemetery was established new. A new cemetery has been in use since 1875.

During the Nazi occupation, both cemeteries were partially destroyed, and the tombstones were used for the construction of the barrier around the city. After 1945 the cemetery was renovated, and the monuments were put in place. In 1992 a new cemetery vandalism occurred: about 80 gravestones were desecrated Nazi symbols.

Cemetery Eisenstadt is different from the other ancient Jewish cemeteries lack of vegetation. However, it is very similar in shape and appearance with the Vienna cemetery. This is due to the fact that the first settlers were the Viennese emigres. Before the entrance to the old cemetery was made through the beautiful semicircular metal gates, but now they have not been preserved. Both cemeteries are open to the public.