The Department of Health is headed by the District Health Officer whose mandate is guided by the District 5 Year Strategic Plan that focuses on the achievement of equity through increased access to Minimum Health Care Package (MHCP), Quality care, efficiency accountability and transparency. 

The overall goal of the department is to provide good quality services to the people of Budaka district in particular and Uganda in general so as to make them attain good standards of health in order to live a healthy and reproductive life.  The objective is to reduce morbidity and mortality from the major causes of ill health and premature health and disparities therein". The Local Government health function is to provide primary healthcare services.

This is achieved through the following outputs: healthcare management services, medical supplies for health facilities, health promotion services, promotion of sanitation and hygiene, NGO basic healthcare services, basic healthcare services among others. Budaka district has 22 health facilities of different categories of which 13 are Government by establishment and 6 are NGO by establishment. The District has no Government hospital. For the Government established health facilities, 6 are at HC level II, 15 are at HC level III and only 1 HC level IV. All the 6 NGO health facilities are at level III including Riverside Hospital. The distribution is fair to the extent that only two sub-counties of Nansanga in Budaka County and Mugiti in Iki-Iki county do not have Government established health facilities. However, some of the health facilities lack basic equipment to offer reasonable basic healthcare services. Many health facilities require rehabilitation and equipping. Besides diseases, poor nutrition has contributed to worrying situation. Because of cross cutting nature of health issues, there is need for an integrated approach to health.

There are various NGOs both Local and International that are involved in AIDS prevention and control in the district. Such activities include blood screening and counselling, medical treatment, home care, health education, AIDS research and orphan support. The implementing partners include SDS-USAID, Global fund and WHO for budget support. Rain Uganda, STAR-E-USAID, TASO, Childfund, Leonard Cheshire, Kadama Widows and Action-Aid Uganda for off-budget support.

Health Infrastructure
This section classifies the distribution of health facilities within Budaka district.
Over the years, since the inception of the District in July 2006, infrastructural development and improvement in the existing Government aided health facilities was one of the overarching priority of the District health sector.

Each health facility has at least one Out-Patient-Department (OPD) on top of other health infrastructure. The number, size and type of infrastructure on any given health facility depend on grade or level in the health hierarchy of the minimum health care package for Uganda. HCII has only an OPD, HCIII has OPD and Martenity, HCIV has OPD, Martenity and a sergical operation threatre. At the District headquarters, a District medical store was built under equalisation grant and PHC development.

It can be observed that all the 13 government aided health facilities at various levels of service delivery have out patient health facilities (OPDs). There are only two sub-counties of Nansanga and Lyama which are not served with OPD facilities. Most health facilities have only one block of housing unit to accommodate 1-2 health staff except Budaka HCIV with 13 blocks. Butove HCII in Lyama sub-county does not have any staff house.

This makes it very difficult to provide emergency services by health workers on call. The status of beds for both adults and children is presented in table for each facility. Apart from Budaka HCIV, Kamonkoli HCIII, Iki-Iki HCIII and Kameruka HCIII, most health facilities have less than 3 beds for adults and 3 for children. Therefore, in-patient services are minimally provided in the District health system. Therefore, there is urgent need to plan and procure patient beds for children and adults and for delivery for expecting mothers. Acute shortage of beds is in Lyama HCIII, Naboa HCIII, Katira HCIII, Kerekerene HCIII, Kaderuna HCIII and Namusita HCII.

The status of wards is very poor in all Government aided health facilities. Budaka HCIV has only one general ward to accommodate male and female adults together with children. There is only one martenity ward in Budaka HCIV. However the District has taken an initiative to construct martenity/general wards in all HCIII with funding from EDF-EU, NUSAF and PRDP. So far, the following health facilities have benefited from the initiative: Iki-Iki HCIII under EDF which was constructed under Pallisa district, Kameruka HCIII and Kamonkoli HCIII which was constructed under NUSAF, Sapiri HCIII, Katira HCIII and Kerekerene which was constructed under PRDP and, Budaka HCIV, Lyama, Naboa and Namusita HCII which was built under PHC development. Kebula HCII and Butove HCII are yet to receive martenity/general ward. In total, there are 11 martenities/general wards in the 13 Government aided facilities. The health service delivery is constrained by transport facilities for emergency cases of delivry. Budaka HCIII has two pick up trucks to provide ambulance services. For lower health facilities, the situation is worse. All the 12 health facilities do no have motorcycles and bicycles for outreach services.