The health system is decentralized and divided into four levels: The central, state, county and community level. Each level has clearly defined roles, capacity and functions which aim to involve local decisions in the overall management of the resources.

The government of South Sudan has declared that basic health and emergency services should be free for all citizens in public facilities. However, the prolonged conflict has significantly reduced the proportion of government spending towards the health system from 8.4% to 2.2% in 2012. The shortage of funding has forced the majority of the populous to buy supplies from the private sector whereby 92.5% represents out-of-pocket (OOP) expenditure. The presence of private health insurance is very minimal, only covering 5.4% of the population while the rest of the health services are funded by NGOs.