In 1647 the town of Eisenstadt was under the rule of the princely house of Esterhazy that had a great influence on the city and led to positive changes. In 1648 by Emperor Ferdinand III Eisenstadt became a free city by paying the repurchase price in the amount of 16,000 guilders and 3,000 barrels of wine. In 1670 Paul I allowed to stay in Eisenstadt and six nearby settlements of 3,000 Jews who were expelled from Vienna. Rabbi of the city was Samson Wertheimer, which itself was buried at the old Jewish cemetery.

There is a need in the graveyard. So there was the old Jewish cemetery in the 17th century near the Jewish quarter. The old cemetery was in operation from 1679 for years 1875 and consisted of about 1140 gravestones only with inscriptions in Hebrew. Due to limited space, near the old cemetery was created new. The new cemetery was in use since 1875.

During the Nazi occupation of both cemeteries were partially destroyed, and the tombstones were used for construction of the barrier around the city. After 1945, the cemetery was renovated and its monuments were set in place. In 1992, a new cemetery has been vandalized: about 80 tombstones were desecrated with Nazi symbols.

Cemetery in Eisenstadt differs from other ancient Jewish cemeteries lack of vegetation. However, it has a great resemblance in form and appearance with the Vienna cemetery. This is because the first settlers were Viennese émigrés. Before the entrance to the old cemetery was made using beautiful semi-circular metal gates, however, at the present time they have not survived. Both cemeteries are open to the public.