The main aims of international cooperation of the FMHS were to exchange scientific, educational and therapeutic information and to develop working contacts between military medical, medical educational and research institutions of the NATO and EU countries as well as civilian medical institutions with educational, defence research and development programmes. Residency and exchange programmes for numerous students, doctors and research workers took place at those institutions.

As for study programmes, the Faculty keeps close relations with partner educational institutions above all in NATO and EU countries. Every year there are exchanges of not only students but also of pedagogical staff with the Military Medical Academy (ESSA) in Lyons in France, contacts in pedagogical sphere are kept with partner schools in Germany (Sanitätsakademie der Bundeswehr, Munich), the Military Medical Academy in Sofia, Bulgaria. In the past there were contacts with schools in Lódź (Poland) and Beograd (Serbia). Students take part in study stays in France, Slovakia, Germany, Sweden, Switzerland, England and in the frame of Erasmus programme in other states.