The Rector and the Vice-rectors administer all educational operations, scientific operations, medical operations, international operations, as well as economic and administrative activities. The Departments are run by the Departments' Heads. Council of the Academy and Colleges solve the fundamental issues of the Academy's activities.

The structure of the Academy consists of 6 Colleges:

• Surgical
• Internal Medicine
• Pediatric
• Biomedical
• Public Health
• Dental