Malaria is the leading cause of morbidity and mortality in South Sudan. It is a major public health issue and is endemic in all parts of South Sudan, with the entire population at risk. Malaria accounts for 45% of all visits to health facilities and 9% of all hospital admissions.

It remains one of the biggest causes of illness and death in children under five. WHO estimates a decrease of 20-40% in malaria mortality rates in the period 2010-2015.

Progress made


Area of improvement


Insecticide treated nets (ITNs) distributed in 2017-2018.


Coverage of intermittent preventive treatment in pregnancy (increased from 32% in 2013 to 57% in 2017 (against a 2016/17 target of 50%)


Decline in the ownership of at least one ITN per household – 66% (2013) to 63% (2017) against a target of 75%.


Percentage of children under 5 years receiving any ACT (increased from 20% in 2013 to 61% in 2017 against a 2016/17 target of 60%)

Malaria remains endemic throughout the country and is a major public health issue, particularly among children under five years old and pregnant women. The 2017 South Sudan Malaria Indicator Survey (SSMIS) indicated that vector control, intermittent preventive treatment of malaria in pregnancy (IPTp), use of rapid diagnostic tests (RDTs)/microscopy and treatment with ACTs have achieved impact.

For example, the SSMIS shows 63% of households having access to at least one insecticide treated net against a 2017 target of 75%.

The survey also showed higher coverage of 84% in Protection of Civilian sites (administered by the UN), and 75% of households in internally displaced person sites (managed by various humanitarian agencies) had at least one insecticide treated net. IPTp coverage increased from 32% in 2013 to 57% in 2017.

Whilst the performance framework does not include targets related to malaria testing for children, parasitological testing of malaria in children under five years old increased from 28% (2013) to 48% (2017). This was mainly due to the availability and use of RDTs and microscopy provided by the Global Fund and other partners.

Although accurate national malaria case management data remains a challenge, WHO estimates a 20-40% decrease in malaria mortality rates in the period 2010-2015. The country aims to reduce mortality by 80% by 2021, which will be challenging given current performance.