Uganda's health system is composed of health services delivered to the public sector, by private providers, and by traditional and complementary health practitioners. It also includes community-based health care and health promotion activities.

The not-for-profit providers are run on a national and local basis and 78% are religiously based. Three main providers include the Uganda Catholic Medical Bureau, Uganda Protestant Medical Bureau, and the Uganda Muslim Medical Bureau. Nongovernmental organizations have emerged as the prominent not-for-profit organizations for HIV/AIDS counseling and treatment. The for-profit providers include clinics and informal drug stores. Formal providers include medical and dental practitioners, nurses and midwives, pharmacies, and allied health professionals. Traditional providers include herbalists, spiritual healers, traditional birth attendants, hydro therapists, etc.

Uganda's health system is divided into national and district-based levels. At the national level are the national referral hospitals, regional referral hospitals, and semi-autonomous institutions including the Uganda Blood Transfusion Services, the Uganda National Medical Stores, the Uganda Public Health Laboratories and the Uganda National Health Research Organization (UNHRO). The aim of Uganda's health system is to deliver the national minimum health care package. Uganda runs a decentralized health system with national and district levels.

The lowest rung of the district-based health system consists of Village Health Teams (VHTs). These are volunteer community health workers who deliver predominantly health education, preventive services, and simple curative services in communities. They constitute level 1 health services. The next level is Health Center II, which is an out patient service run by a nurse. It is intended to serve 5000 people. Next in level is Health Center III (HCIII) which serves 10,000 people and provides in addition to HC II services, in patient, simple diagnostic, and maternal health services. It is managed by a clinical officer. Above HC III is the Health Center IV, run by a medical doctor and providing surgical services in addition to all the services provided at HC III. HC IV is also intended to provide blood transfusion services and comprehensive emergency obstetric care.

In terms of governance, the MOH is currently implementing the Health Sector Strategic and Investment Plan (HSSIP), which is the third iteration of health sector strategies. The MOH coordinates stakeholders and is responsible for planning, budgeting, policy formulation, and regulation.

According to a 2006 published report, the health sector at the district and sub-district level is governed by the district health management team (DHMT). The DHMT is led by the district health officer (DHO) and consists of managers of various health departments in the district. The heads of health sub-districts (HC IV managers) are included on the DHMT. The DHMT oversees implementation of health services in the district, ensuring coherence with national policies. A Health Unit Management Committee (HUMC) composed of health staff, civil society, and community leaders is charged with linking health facility governance with community needs.

In addition, the Uganda Medical Association (UMA) seeks to "provide programs that support the social welfare and professional interests of medical doctors in Uganda and to promote universal access to quality health and health care." However, the government's failure to improve the compensation of doctors , as well as failing to conduct a review of the supply of medicines and other equipment in health centres across the country, led to a UMA strike in November 2017, effectively paralysing Uganda's health system.

At the beginning of the 21st century, the government of Uganda began implementing a series of health sector reforms that were aimed at improving the poor health indicators prevailing at the time. A Sector-Wide Approach (SWAp) was introduced in 2001 to consolidate health financing. Another demand side reform introduced in the same year was the abolition of user fees at public health facilities, which triggered a surge in outpatient attendances across the country.