However, in 1918 with the establishment of the independent Republic of Lithuania, the State Council decided to reestablish Vilnius University.

Since Vilnius was later under Polish administration and the Lithuanian government had to be transferred to Kaunas, this decision was not put into effect.

The Lithuanian Provisional Government restored the name of Vytautas Magnus to the university after the Nazi invasion of the Soviet Union in the summer of 1941.

The German occupation government closed the university in March 1943, after Lithuanians refused to form an SS battalion.

The government passed the law on re-establishing the Vytautas Magnus University on 4 July 1989 and the cabinet registered the temporary Statute later that month.

The re-established university was the second in then Soviet-occupied Lithuania, and the first school of higher education that was independent of governmental institutions.

The most important principle in the university's activity became academic freedom, while its main purpose was to prepare graduates with a broad humanistic orientation for Lithuania's needs in research, culture, education and economy.

Particular attention is given to foreign languages and computer skills, making this university different from other schools of higher education in the country.

Master's and Doctoral studies became a priority at the university and demanded a pedagogical staff with high qualifications.