All courses in the college are hosted in respective faculties and departments according to their relevance. The Nairobi campus host headship of all faculties while the rest of the campuses have heads of departments.

The faculty of clinical sciences, the oldest, comprises clinical medicine and pharmacy departments. The faculty of Public Health Sciences has most departments, namely: Environmental Health Sciences; Health Education; Medical Engineering; Community Oral Health and Nutrition. To keep track of medical trends, the faculty of Research and Information was established, with four departments: Medical Education; Health Records and Information; Information Technology and Counselling. Curved from the Faculty of Clinical Sciences, the Nursing Faculty is the newest, and could soon be the biggest. The Faculty of Rehabilitative Sciences includes Dental Technology and Orthopedics Technology departments.

The support and service departments include administration, catering, information technology, skillslab, maintenance, hostels and the library.