Built in the 16th century in the center of Vilnius, reflects Gothic, Renaissance, Baroque, and Classicist architectural styles. The ensemble consists of 13 courtyards, 13 buildings, St. John's Church, and a bell tower. It houses faculties, a library, and the rector's office. In 1985, the university was awarded the European Gold Medal for the protection of monuments, and the complex represents Lithuania in the Mini Europe park in Brussels.

Formed in the 19th century, is a cozy part of Simono Daukanto Courtyard. In the 16th century, buildings donated by patrons served as student dormitories, and the courtyard was used for open theater performances. Now it houses the Institute of Foreign Languages, the departments of the Faculty of Philology, and the auditoriums of the Center for Oriental Studies. The metal gates created by Juozas Kėdainis, installed on the occasion of the university's 400th anniversary, add to the coziness of the courtyard.

Previously, this courtyard housed dormitories for poor students and the homes of musicians from Vilnius Cathedral. At the beginning of the 19th century, a three-story building with a courtyard was constructed, and at the beginning of the 20th century, amenities and apartments were added. After reconstruction in 2005, the Faculty of Philosophy moved in, and a royal beech tree was planted in the courtyard.