Following the Soviet invasion of Poland in September 1939, the university was briefly administered by the Lithuanian authorities (from October 1939), and then after Soviet annexation of Lithuania (June 1940), punctuated by a period of German occupation after Operation Barbarossa, from 1941 to 1944, when it was administrated as the Vilnius State University. In 1945, the Polish community of students and scholars of Stefan Batory University was transferred to Nicolaus Copernicus University in Toruń. After Lithuania regained its independence in 1990, following the dissolution of the Soviet Union, it resumed its status as one of the prominent universities in Lithuania.