Muhimbili National Hospital has eight (8) Directorates with six (6) units named;

1. Directorate of Medical Services
2. Directorate of Surgical Services
3. Directorate of Clinical Support Services
4. Directorate of Nursing and Housekeeping Services
5. Directorate of Technical Services
6. Directorate of Finance and Planning
7. Directorate of Information and Communication Technology
8. Directorate of Human Resources

Six units under the Executive Director are;

1. Procurement Management Unit
2. Legal Services Unit
3. Corporate Communication and Customer Care
4. Internal Audit Unit
5. Research, Training and Consultancy Unit.
6. Quality Assurance Unit