The General Jonas Zemaitis Military Academy of Lithuania cooperates with almost all the Lithuanian institutions of higher education. In cooperation with Antanas Gustaitis’ Aviation Institute of Vilnius Gediminas Technical University, it trains aviation specialists for the Lithuanian Armed Forces and exchanges students with the Institute of International Relations and Political Science of Vilnius University.

The military and civil personnel of the Academy participate actively in the events organized by different organisations. The cadets constantly help the Lithuanian Riflemen’s Union in organising camps and conducting exercises for the young riflemen and the scouts.

The schoolchildren and students are always very welcome to the Academy. Here they go on the excursions and attend exhibitions. The cadets often go to the meetings with schoolchildren and school-leavers at the secondary schools and gymnasiums to introduce them to the procedures of the admission and studies at the Academy, peculiarities of service, and the cherished traditions at the Lithuanian Armed Forces.

Since 2002 the cadets have been participating in the programme Civic Cadets’ Education in the Voluntary Activities of Big Brothers, Big Sisters. This long-term project is a sincere and voluntary friendship between the cadets and socially vulnerable children and their families. 

On 3 March 2009, the Military Academy of Lithuania and public body Gimnazistai signed a social partnership agreement, under which the Academy has been participating in the joint projects for children and youth’s civic and patriotic education as well as for fostering their physical and spiritual wellness.

On 27 May 2009, the Military Academy of Lithuania and Vilnius City Municipality entered into a cooperation agreement, under which both institutions undertook to organise joint educational, civic education, art and science projects as well as public events in the public and cultural environment and at the Academy.   

On 1 January 2010, the Military Academy of Lithuania and the Border Guard School of the State Border Guard Service concluded a cooperation agreement, under which both institutions help each other in cadet and border guard training while preparing common training material, exchanging the specialists and allowing the cadets the possibility to do training at the Border Guard School. It is planned to organise common training and sporting and professional excellence competitions. 

In 2010 the Academy signed the cooperation agreements with the following educational institutions: Verkiai Special School in Vilnius, Adolfas Ramanauskas-Vanagas Gymnasium in Alytus, and Secondary School No. 2 in Kalveliai. The agreements aim to encourage greater cooperation between the cadets and schoolchildren as well as mutual participation in the events organised by the educational institutions. 

On 1 July 2010, the Academy and Mykolas Romeris University has started the cooperation with the project Infrastructure Development for the Social Sciences Studies that both institutions undertook to set up and implement. 

On 11 January 2011, the Academy and the Lithuanian University of Agriculture signed the cooperation agreement with the aim to set up and run the joint project Research on the Use of Biofuel and Alternative Fuel for Diesel Engines. 

On 19 January 2011, the General Jonas Zemaitis Military Academy of Lithuania, Klaipëda University, Kaunas University of Technology, and Vytautas Magnus University concluded a joint activity agreement on doctoral studies in the field of Political Science. 

On 21 January 2011, the Academy started the cooperation with the ancient Balts’ fight fraternity Vilkatlakai. Under the agreement, the Academy and the fraternity participate in common events and archaeological investigations and aim to restore the ancient armament and carry out practical experiments.

On 14 March 2011, the Academy and Mykolas Romeris University signed another cooperation agreement under which the mutual participation in the projects and exchange of students, cadets and lecturers was initiated. 

The Military Academy of Lithuania also cooperates with Trakai History Museum, Vytautas the Great War Museum in Kaunas and other public organisations.