The oldest written data about Kairėnai Manor dates back to 1545, it is the privilege of Sigismund the Old, who gave three posts in Kairėnai to Jarmala, so Kairėnai could have been a part of the state manor or a manor of the grand dukes.
In 1692, Kairėnai Manor was bought by Jan Kazimierz Sapieha, the voivode of Vilnius and the hetman of the Grand Duchy of Lithuania. Four generations of this noble family ruled the manor. In 1730-1759, Kairėnai Manor was leased to the monks of the Trinitarian Order of Antakalnis.
In 1759, a priest and later a bishop Jan Dominik Łopaciński took the manor over from the monks. In 1817, the manor became the property of J.M.A. Łopaciński. Thanks to his wife Dorotea, the life of the manor became much more lively. It hosted public figures, it had an orchestra, an amateur theatre, and a rich library. It had a well-groomed English-style park with a pond system, a summer theatre pavilion, a gazebo on the island, a Baroque chapel, a fountain, flowers, etc.
During the German occupation, for a short period of time, Kairėnai Manor housed a school. During the First World War, the palace burned down. After the war, the remains of the palace, the oficina and some other buildings were demolished.
In 1974, the entire Kairėnai Manor homestead with almost one and a half hectares of land was transferred to Vilnius University for the creation of the Botanical Garden. The first historical and archaeological research was carried out and the manor ensemble was declared an architectural monument. Kairėnai Botanical Garden, that currently operates here, has a vast collection of plants.