The sector mandate is to reduce morbidity and mortality from major causes of ill health of the people in the district and the nation at large. The sector is composed of administration (DHO), health education, drug inspection, reproductive health, TB, leprosy / neglected diseases and environmental health. The sector partners with STAR SW, SEARCH, SDS, USAID Rhites and TASO Rukungiri in activities like TB/HIV plus Safe male circumcision services, HIV/AIDS and counseling services, data collection on health services and HIV/AIDS and counseling services respectively. This has helped mostly in the reduction of HIV prevalence rate to 3.6% which is lower than the national. The sector plans to increase sensitization of the community, accredit more health centers to provide ART services and carry out HIV/ART outreaches to extend services closer to the communities in a bid to continue reducing HIV spread rate.

Mitooma district has no hospital; it has one health centre IV, 6health centre IIIs and 8health centre IIs. They are all instituted by the district local government.