He was the father of art historian and critic Jurgis Baltrušaitis Jr. Baltrušaitis was born to a family of farmers in Paantvardys village near Jurbarkas, which was then under Imperial Russian rule.

Between 1900 and 1914, Baltrušaitis lived in Italy and Norway and spent much time traveling in other countries in Western Europe.

During World War I and the subsequent Russian Revolution he was in Russia, where he actively participated in the Lithuanian political struggle for independence.

Following the annexation of Lithuania by the Soviet Union, his son, Jurgis Baltrušaitis Jr., an art historian and art critic, served as a diplomat for the Lithuanian diplomatic service which continued to represent Lithuanian interests in some Western countries.

Baltrušaitis Sr. died in Paris in January 1944; he is buried at Montrouge Cemetery.