On December 13, 1939, the Seimas of the Republic of Lithuania adopted the Law on Universities, stipulating that, in addition to Vytautas Magnus University, Lithuania had one more university – Vilnius University. This change was determined by the recovery of Vilnius and the decision to have a Lithuanian university in Vilnius. It was decided to transfer the staff and students of the faculties of Humanities and Law from Kaunas to Vilnius.
During the first Soviet occupation, Vytautas Magnus University lost its autonomy and was renamed University of Kaunas on August 21, 1940. The university started a new academic year losing a recently closed Faculty of Theology and Philosophy and the Faculty of Mathematics and Natural Sciences, which was transferred to Vilnius University.
On August 1, 1941, during the Nazi German occupation, the Provisional Government of Lithuania approved the Statute of the University and renamed the university back to Vytautas Magnus University. Although the university was formally closed down by the occupying authorities in March 1943, it operated for another year.
In the autumn of 1944, with the beginning of the second Soviet occupation, Vytautas Magnus University was allowed to start a new academic year. In July 1946, when the university was put under the authority of the Ministry of Higher Education of the Soviet Union, its name was changed to Kaunas State University.
In 1949, Kaunas lost the core of the humanities – the Faculty of History and Philology was transferred to Vilnius University; moreover, the largest university library in Lithuania, containing the largest number of rarities, was disassembled. Finally, on October 31, 1950, the Minister of Education of the USSR reorganized Kaunas State University into Kaunas Polytechnic Institute and Kaunas Medical Institute.

University of Lithuania/Vytautas Magnus university in 1930–1940s
Due to the Second World War and the occupations, a significant part of the Lithuanian intelligentsia was forced to leave Lithuania. The diaspora included a number of former teachers and students of Vytautas Magnus University. For several years, they gathered in DP (displaced persons) camps in Germany and Austria, and later settled in the United States, Canada, Australia, and other countries; however, they retained memories of the interwar university and formed various organizations.
Some of the former professors of Vytautas Magnus University became members of the Association of Lithuanian Professors in Chicago, and some of the pre-war student organizations (Student Scout Corporation “Vytis”, Corporation of Student Reservists of Vytautas Magnus University “Ramovė”, National Student Organization “Neo-Lithuania”, Catholic Federation “Ateitis” and others) were restored. Senior former students and employees of Vytautas Magnus University, as well as young members who had already studied in the post-war years often worked together in the associations. This made it possible to pass on the memories of the interwar university and the obligation for the younger generation to return to it.
At the initiative of Kaunas scientists and intelligentsia and the Reform Movement of Lithuania “Sąjūdis“, the issue of re-establishing Vytautas Magnus University was raised in 1988. Diaspora scientists have also been actively involved in the re-establishment of the university.

Members of the Re-establishment Senate of VMU in 1989.
On March 30, 1989, Kaunas scientists elected the Re-establishment Council of Vytautas Magnus University, instructing it to prepare a temporary statute and address other issues related to the re-establishment. On April 28, the act of re-establishing Vytautas Magnus University was proclaimed at a conference of Lithuanian and diaspora scientists, and on July 4, the Supreme Council passed the law reestablishing the university.
At the end of December 1990, the Re-establishment Senate adopted a statute legitimizing the principles of university autonomy, academic freedom and the unity of science and studies, a three-cycle study system awarding Bachelor’s, Master’s and Doctoral degrees, and the artes liberales study model.