In 1737 the ruler Augustus III with the privilege invited Jews to settle in Joniškis. In 1795 sources mentioned that 88 Jews lived in the city. A couple of years later, the growing community received permission to build a synagogue, along with a plot of land for a cemetery a bit more remote form the city.
The cemetery is 1000 meters northeast of Joniškis, 210 meters northwest of the road Joniškis–Skilvioniai. This cemetery dates to the beginning of the 19th century and the history of the Jewish community in Joniškis. There are extremely well-preserved tombstones here. The cemetery has about 800 different shapes of pink, grey, black granite, concrete tombstones mostly with engraved memorial inscriptions in Hebrew, several brick burials vaults. The oldest tombstone dates to 1806. In 1897, a little more than a hundred years later, Joniškis had 4,774 inhabitants, of whom 2,272 were Jews. In the interwar years, due to the increasing migration of Jews to the United States, then Palestine and the Union of South Africa, the community began to retreat. In 1936 only about 700 Jews lived in Joniškis. Jews were engaged in various activities, a significant number of them were engaged in trade and crafts.
Also, are mentioned as watchmakers, barbers, hatters, carpenters, butchers, and doctors, from whom Gitelis ir Jokūbas Garberiai were very famous in Joniškis region. In 1941 summer after Nazi Germany occupied Lithuania, the persecution of the Jews of Joniškis soon began the community was destroyed during the Holocaust.