The history of the University of Vilnius has been inseparably connected with the Jesuit Order for more than two hundred years, which already in 1565 conceived the idea of establishing a university in the capital of the Grand Duchy of Lithuania.

Initially, the order wanted to choose Krakow as its main centre, but as a result of opposition from the Jagiellonian University authorities and after encouragement from Stefan Batory, the Jesuits chose Vilnius. Its location made it easier to carry out missions to the nearby eastern areas with a predominantly Orthodox faith, and it was also intended to "embrace Moscow, China and Tartary". The fact that Vilnius was at that time the centre of a strong Protestant movement in the Grand Duchy of Lithuania also had a mobilising effect on the monastic superiors. An additional favourable factor was the lack of universities in Vilnius, which in turn provided opportunities to develop an educational centre for the Lithuanian lands.

The Jesuits arrived in Vilnius in 1568, and with the outstanding help of King Sigismund Augustus and Vilnius Bishop Valerian Protashevičius, they received the St John's Parish Church, which became the Order's main shrine for almost two centuries. Describing the building of the Vilnius ensemble in a letter to the Order's general in 1570, the Austrian provincial said that he "does not know of a college in Italy that could match it". Within a short time, the school run by the monks began to influence the whole province (including Mazovia and Warsaw).

Stefan Batory, a great promoter of the Jesuits, approved the act of foundation of the university in 1579, and the bull of Pope Gregory XII, authorising the transformation of the college into a university, indicated that its structure was to be modelled on the Roman College. Stanislaw Wierszewicki became the first rector, followed by Jakub Wujek and, from 1579, Piotr Skarga. The Vilnius university attained a very high rank, taking over the role previously played by the Krakow and Königsberg academies. New faculties were created, new university buildings were erected and hundreds of graduates left its walls. The university's activities included the establishment of an astronomical observatory, the development of the chemical sciences department, a theatre and a printing press. In 1782, following the reforms carried out by A. Poczobut-Odlanicki at the behest of the National Education Commission, Vilnius Academy was transformed into the Main School of the Grand Duchy of Lithuania.

As a result of changes in the structure of teaching in the Russian Empire, it was transformed into the Imperial University of Vilnius in 1803. It was the largest university in the whole country, and the working professors made it the centre of scientific and cultural life not only of the lands of the Russian partition. For many years, the curator was A.J. Czartoryski, the rector (1806-1814) was Jan Śniadecki, and the lecturers included: S.B. Jundziłł, Jędrzej Śniadecki, G.E. Groddeck, I. Danielewicz, J. Gołuchowski, I. Daniłowicz, J. Lelewel, M. Bobrowski, J. Frank. This most splendid period in the university's history was interrupted by Nicholas I's restrictions after the November Uprising. At that time, the university was closed down, limiting the possibility of studying to the established Medical and Surgical Academy and Theological Academy, which were also closed down after ten years.

In 1919, the Polish authorities reactivated the university under the name of Stefan Batory University in Vilnius with six faculties, where eminent professors, such as: L. Kolankowski, S. Kościałkowski, H. Łowmiański, S. Srebrny, J. Otrębski, O. Chomiński, W. Taszycki, H. Turska.

Since 1939 Vilnius University has operated as a Lithuanian university and a large part of the Polish faculty moved to Toruń, co-founding M. Kopernik University. Today, a large part of the buildings of the former Jesuit academy still perform their teaching functions, and Vilnius University is the largest university in the Republic of Lithuania.