The Jews in the Šėta settlement were mentioned for the first time in 1709. In 1766, they got the privilege to build a synagogue. A synagogue and Beit Midrash (a learning house) were destroyed during a fire in 1878. In 1893, architect Nikolay Andreyev developed a project of a new synagogue and Beit Midrash in one building. The building was damaged during World War I – a roof collapsed, a center of the western part was destroyed. During reconstruction in 1920, this part of the synagogue was divided into two buildings – two separate premises on the ground floor were allocated for women. During the interwar period, the synagogue housed a Jewish primary school and a bank. When the Nazis took over Šėta, the settlement’s residents Jews were driven into Kėdainiai ghetto and murdered together with Jews of Žeimiai and Kėdainiai in Daukšiai village on August 28, 1941. The building of the synagogue remained without a community, after layout change and connection of blocks of the western part was adapted for Šėta Secondary School.