In XVI–XVII th centuries the area in Antakalnis district, where the building complex of the General Jonas Žemaitis Military Academy of Lithuania is located today, belonged to the noblemen Sapiegos. Even today a Baroque palace (XVII c. last decade)  built by the Grand Etymon of the Great Duchy of Lithuania Kazimieras Jonas Sapiega, God Jesus Church, Trinitory Monastery, other buildings and part of the park are located in  the neighbourhood of the Military Academy. The palace got its present looks after reconstruction in the middle of XIX th century for it was damaged during the Rebellion in 1794. From the end of XVIII c. military hospital, barracks, and other military facilities of Czar Russian Army (in 1812 France Army leaded by Napoleon) were located in this complex.

In 1861–1863 Cadet Corps of Emperor Alexander were located here (Rus. Александровский Брест-Литовский кадетский корпус)

In 1919–1939 the Complex belonged to Polish Armed Forces and Vilnius University Clinics.

In 1940 Military School was moved from Kaunas to Vilnius and turned into Soviet Vilnius Infantry School that existed in 1940–1941 and 1945–1953.

Since 1953 Soviet Higher Education Anti Air-Craft Defence Radio Electronic School was located here.

In 1992 National Defence School of Lithuanian Armed Forces was established in the place which was reorganized into Military Academy of Lithuania in 1994.