Headquarters

• Rector and deputies
• Secretariat
  
• Bursar Division
• Planning and Organisation Office
• Development and Management Support Office
• Office for Studies
• Science and Research Office
  
• Information Security Office
  
• Student regiment
  

Faculty of Military Leadership (Brno)

• Department of Quantitative Methods (K-101)
  
• Department of Resources Management (K-102)
  
• Department of Leadership (K-104)
  
• Department of Military Science Theory (K-105)
  
• Department of Fire Support (K-107)
• Department of Engineer Support (K-108)
• Department of Logistics (K-109)
• Department of Tactics (K-110)
  
• Department of Intelligence Support (K-111)
  

Faculty of Military Technology (Brno)

• Department of Weapons and Ammunition (K-201)
• Department of Combat and Special Vehicles (K-202)
  
• Department of Engineer Technology (K-203)
• Department of Air Force (K-205)
• Department of Aircraft Technology  (K-206)
• Department of Communication Technologies, Electronic Warfare and Radiolocation
  (K-207)
• Department of Air Defence (K-208)
  
• Department of Informatics and Cyber Operations (K-209)
• Department of Military Geography and Meteorology (K-210)
  
• Department of Military Robotics (K-211)
  
• Department of Mathematics and Physics (K-215)
  
• Department of Mechanical Engineering (K-216)
• Department of Electrical Engineering (K-217)
  

Faculty of Military Health Sciences (Hradec Králové)

• Department of Epidemiology (K-301)
• Department of Military Medical Service Organisation and Management (K302)
• Department of Radiobiology (K-303)
• Department of Toxicology and Military Pharmacy (K-304)
• Department of Military Surgery (K-305)
• Department of Military Internal Medicine and Military Hygiene (K-306)
• Department of Emergency Medicine and Miltary General Medicine (K-307)
• Department of Molecular Pathology and Biology (K 308)

Centre for Security and Military Strategic Studies

Language Centre (Brno)

Physical Training and Sports Centre (Brno)

NBC Defence Institute (Vyškov)