Jews settled in Pakruojis in the middle of the 18th century. As early as 1765 420 Jews were living in town. In 1801 the first wooden synagogue in Lithuania was built on the bank of the river Kruoja. In the 19th century, there were 50 wooden houses, 12 warehouses, and 4 smithies in Pakruojis. As the Jewish community grew, the first Jewish cemetery was established in Pakruojis (at the end of today’s Darius and Girėnas Streets) in 1800. This Jewish cemetery is located a little further away from the town of Pakruojis and was established much later. Members of the community were not buried here until the 20th century. The total size of the cemetery is more than 100 meters long and about 40 meters wide. Unfortunately, this Jewish cemetery was not in use for long until 1941.

After the Nazis invaded Pakruojis, the cemetery was desecrated by letting animals graze there. When the Soviets occupied Lithuania, the cemetery was destroyed. It is said that some of the monuments were used to demolish the yard of the Pakruojis mill. Today the natural boundaries are open fields on three sides and the Pakruojis road on the fourth. The entire area is overgrown with trees and is now surrounded by a blue fence. There are about fifty grave stones in total, of which about thirty are in the fenced area and twenty are outside the fence. In 2011, the cemetery was reconstructed on private initiative. Now it is looked after and managed by the Pakruojis municipality.