The manor at Babtynas village was set up already at the 16th century by the Šiukštai family. Later the manor belonged to Andrius Vilimavičius and Jokūbas Sauginavičius. In the 18th century, during the rule of the Prozor family, Babtynas became a representative manor.
In 1797, Babtynas was sold to Burhard fon Korf. Shortly after that it was acquired by the dukes Giedraičiai who owned it until 1830. Then the manor was purchased by the Counts Benedyct Emmanuel and Vanda Tyszkiewicz. The Tyszkiewicz family ruled here until World War I. In the interwar period, the household and cultural traditions were cherished by General Vladas Nagevičius (1881–1952) who received the land in reward for creating the Lithuanian army.
World War II disrupted the flourishing of the manor. During the Soviet occupation, it housed an office of the collective-farm ward and a multi-dwelling house.
Since 1999, a new stage of the manor life commenced when the remaining buildings were acquired by Mindaugas Šventoraitis who adapted it for residence and cultural activity.