The rector is the head of the University of Veterinary and Pharmaceutical Sciences Brno. Subordinate to the rector are three vice-rectors - vice-rector for education, vice-rector for science, research and foreign relations and the vice-rector for strategy and development of VFU Brno. The bursar handles the economic affairs, the chancellor manages the administrative dealings of the university. Self-governance at the university is provided by the University Academic Senate. The university body is the VFU Brno Board of Supervisors. Issues concerning education and scientific activity are discussed in the University Scientific Council.
The university is divided into the Rectorate, including the Rector´s Office and other working locations, and two faculties - the Faculty of Veterinary Medicine and Faculty of Veterinary Hygiene and Ecology.