[2] It is named in honor of General Jonas Žemaitis, commander of the armed anti-Soviet resistance in Lithuania.

On 16 December 1992, by order of the government, the National Defense School was established under the Lithuanian Armed Forces.

Commandants of the academy were:[5] The academy delivers internationally recognized bachelor's, master's and doctoral education to members of the Lithuanian defense and national security community, and offers multiple professional military education, language, and national security training courses.

The academy campus covers a territory of 5 ha in the Vilnius neighborhood of Antakalnis.

The academy participates in the European Initiative for the Exchange of Young Officers (sometimes referred to as "Military Erasmus" or EMILYO), a network of 65 military higher education institutions, and implements international semesters for officer-cadets with participants from Austria, Belgium, France, Italy, Poland, USA and other countries.