Professor Jean-Emmanuel Gilibert founded the Vilnius University Botanical Garden in 1781 in the courtyard of the Medical College, now 22 Pilies Street. The Garden occupied an area of about 200 square meters and contained about 500 species of plants grown outdoors and in a small greenhouse. Funds raised by the famous naturalist and companion of James Cook, Johann Georg Adam Forster, contributed a lot to the land's acquisition in Sereikiškės at the foot of the Castle Hill.

In 1799 the Botanical Garden moved to a new site with an area several times larger than previous site. Professor Stanislaw Bonifacy Jundzill headed the garden for 25 years. Under his management by 1824 the collections of the Garden contained as many as 6,565 taxa.

Botanical Garden closed and reopened

The Russian administration closed Vilnius University in 1832 after the Uprising of the previous year. The Vilnius University Botanical Garden stayed open for 10 more years until 1842 when it shut down completely. Introduced plants perished without proper maintenance and the Botanical Garden soon turned into just another park.

The Botanical Garden was successfully re-established in 1919 at the new place of the Vingis Estate, in the valley of the Neris River in the western part of Vilnius. Earlier known as the Department of Plant Systematics and Geography, the Vilnius University Botanical Garden in Vingis was in 2011 renamed Vingis Department. Today it houses as many as 4,600 different plant species and cultivars in greenhouses and outdoors.

In 1974, just before the 400th anniversary of Vilnius University, the expanding Botanical Garden moved to a new site in the village of Kairėnai, to a site of the previous wealthy Estate, in the north-east of Vilnius. The Botanical Garden in Kairėnai and Vingis occupies a total of 199 hectares (about 2 square kilometers).