The Department has a mandate to provide comprehensive, integrated public health services to residents of the FCT.
It is responsible for health education, family planning, environmental and occupational health, control of disease spread through programmes like Roll Back Malaria Initiative, Onchocerciasis Control and Blindness prevention, TB and Leprosy prevention.

The Department also works in collaboration with various donor agencies that support public health care programmes. These include UNICEF, WHO, Partnership for the Transformation of Health Systems (PATHS), The Leprosy Mission Nigeria, (TLMN) and the Christopher Blinden Mission (CBM).

The Public Health Department has the following Divisions and Units:
1. Environmental/Occupational Health Division
• Occupational Health Unit
• Environmental Health Unit
• Health Promotion & Health Education Unit

2. Epidemiology Division
• Survey Unit
• M & E Unit
• International Health Unit
• Disease Surveillance and Epidemic Management Unit
• Public Health Laboratory Unit

3. Disease Control Division
• Tuberculosis and Leprosy Control Unit
• Onchocerciasis Unit
• Schistosomaisis Control & NTDS Unit
• Roll Back Malaria Programme Unit
• Non-Communicable disease control Unit
• HIV/AIDS Unit