
In 1940 Lithuania was annexed to the Soviet Union in the wake of the Soviet-German (Molotov-Ribbentrop) non-aggression pact. The annexation of Lithuania led to the nationalization there of private property, which was largely owned by Jews. The nationalization, that affected factories and large stores owned by Jews, was paralleled by the closure of Jewish educational institutions in the town and the curtailment of Jewish cultural and political activity.
The German army occupied Pilviśkiai on June 23, 1941. Under German rule the local Lithuanian police immediately began persecuting the Jews. During August and September 1941 the Germans and their Lithuanian accomplices murdered all the Jews of the town.
Pilviśkiai was liberated by the Red Army in the summer of 1944.