In the year 1966, the first government hospital, Oshakati hospital, was inaugurated in northern South-West Africa. It was constructed by the apartheid regime of South Africa which was occupying the territory. Prior to this inauguration, Finnish missionaries had, for 65 years, provided healthcare to the indigenous people in a number of healthcare facilities of which Onandjokwe hospital was the most important. This article discusses these two agents’ ideological standpoints. The same year, the war between the South-West African guerrillas and the South African state started, and continued up to 1988. The two hospitals became involved in the war; Oshakati hospital as a part of the South African war machinery, and Onandjokwe hospital as a ‘terrorist hospital’ in the eyes of the South Africans. The missionary Onandjokwe hospital was linked to the Lutheran church in South-West Africa, which became one of the main critics of the apartheid system early in the liberation war. Warfare and healthcare became intertwined with apartheid policies and aggression, materialised by healthcare provision based on strategic rationales rather than the people’s healthcare needs. When the Namibian state took over a ruined healthcare system in 1990, the two hospitals were hubs in a healthcare landscape shaped by missionary ambitions, war and apartheid logic.