Malaria is endemic across South Sudan. It is the leading cause of morbidity and mortality by a significant margin, placing 100% of the population at risk. Overall, South Sudan is among the 22 highest burden malaria countries in the world, accounting for 1.3% of all global malaria cases and deaths in 2020, and 1.2% of global malaria deaths ). In 2020, 5.7% of malaria cases in East and Southern Africa occurred in South Sudan. Between 2017 and 2020, the case burden for malaria increased slightly by 3.3% (from 272 to 289 per 1000 of the population at risk), while deaths also increased slightly by 1.2% (from 0.656 to 0.664 per 1000 of the population at risk.
Although comprehensive data remain limited, what are available indicate significant variations in the malaria burden, by geography, age, sex and socio- economic status. Like other countries in the East Africa region, the malaria burden is highly seasonal, peaking annually during rainy seasons. The impact of these changes is that the majority of counties have been pushed to exceed epidemic thresholds for malaria cases during the July to November period on an annual basis.
Transmission intensity shifted from the southern parts of the country in 2013 to the northwest part in 2017. This migration of intensity has been attributed to a number of factors, including flooding, poor access to health services, comorbidity with acute severe malnutrition, and low coverage of malaria interventions in those areas. The resurgence of armed conflict in 2016 also suspended a number of malaria programme activities, blocked access to health facilities or destroyed them, and increased the problem of regular stock outs of antimalarial medicines. While there has been a recovery of the programme since that time, a number of serious challenges remain that create ongoing gaps. Areas in the north-eastern part of the country, for example, remain insecure, significantly limiting what can be achieved in terms of malaria prevention and control.
In 2013, Plasmodium falciparum was responsible for up to 94% of all morbidity; 5% by P. vivax; and 0.7% by P. malariae. Mixed infections occurred in 6.3% of cases especially in the Greater Equatoria region.  The malaria parasites are transmitted by vectors Anopheles gambiaess, An. arabiensis and An. funestus. 
The national malaria response in South Sudan is led by the National Malaria Control Programme (NMCP). Technical and operational gaps, including insufficient human resources at all levels, significantly limit the ability of the NMCP to provide adequate management and oversight to malaria prevention and control on a country-wide basis. Of the funding available for the national malaria response between 2018 and 2020, 11% came from the Government of South Sudan, 46% from the Global Fund, and the remaining 43% from other partners.
Long-lasting insecticidal nets (LLINs)
Long-lasting insecticidal nets (LLINs) are the main vector control intervention in South Sudan. They are distributed free of charge through mass campaigns and continuous distribution, largely through antenatalcCare (ANC) and the Expanded Programme on Immunisation (EPI) interventions. Ownership of at least one insecticide treated net (ITN) by households declined slightly from 66% in 2013 to 63% in 2017. The 2017 South Sudan Malaria Indicator Survey found that over two-thirds of ITNs (68%) came from mass distribution campaigns. The percentage of children under 5 who slept under an ITN the previous night decreased slightly from 46% in 2013 to 42% in 2017. The percentage of pregnant women who slept under an ITN remained similar over the same period – with 50% in 2013 and 51% in 2017. 
There are significant logistical and socio-behavioural challenges for reaching universal LLIN coverage, including insufficient supplies of nets themselves, challenging terrain for distribution and logistics management, insufficient data to monitor usage, and low levels of knowledge regarding correct and consistent use of nets, partially due to high level of illiteracy and inadequate coverage and continuity of linked social and behaviour change communication (SBCC) interventions. The next mass LLIN distribution is planned for 2023. The will be a follow-up to a campaign in 2020. 
Seasonal malaria chemoprevention
During 2019, seasonal malaria chemoprevention (SMC) was piloted in one county in Western Equatoria with a coverage of 91.1% of the targeted population and adherence rate of 99%. Between 2020 and 2022, the NMCP aims to scale up SMC to cover the rest Western Equatoria and Northern Bahr El Ghazal States.
A key problem in malaria diagnosis is the presumptive treatment of malaria. For instance, more than 50% of malaria cases in children are treated presumptively.  What is more, only 9% of severe malaria was diagnosed in children taken to the health facilities for curative care. 
Malaria treatment is delivered through health facilities and iCCM.  Progress has been made in iCCM, but not all targeted hard-to reach areas have been covered due to limited access to infrastructure and insecurity.  Moreover, implementation strategies across partners are not effectively coordinated because iCCM is run as a vertical programme by NGOs and the NMCP is involved only to a limited extent. 
Malaria in pregnancy
Protecting pregnant women from malaria is done with ITNs and intermittent preventive treatment of malaria in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP)/Fansidar®. WHO recommends that pregnant women receive at least 3 doses starting from the 2nd trimester of pregnancy. Coverage of the first 2 doses of IPTp has generally increased from 2013 to 2017. The percentage of women with a live birth in the previous 2 years who received one dose of SP increased from 38% to 67%, while the percentage of women with at least two doses of SP increase from 32% to 57%. 
However, scaling up IPTp to at least 3 doses of SP, as recommended by WHO, has been challenging. Some of the reasons cited for low coverage include insufficient stocks of the SP, poor access to ANC services, lack of health worker supportive supervision and poor health seeking behaviour. 
Challenges for South Sudan’s public health sector include technical and operational shortcomings, inadequate training, unavailability of job aids at the health facilities and inadequate supportive supervision.  Despite these challenges, a 2017 assessment found that malaria services were generally available, with 95% of all facilities surveyed able to provide malaria diagnosis in some form. Sixty percent of facilities surveyed had trained staff with some knowledge of treatment guidelines, and 25% had at least one trained staff member in IPT.
Medicines and commodities were available in less than half of the facilities. Of the medicines and commodities tracer items, facilities most often had in-stock first-line antimalarial medicines (53%), paracetamol cap/tabs (48%), and IPT drugs (37%). Only 6% of facilities had all malaria service tracer items. However, on average, facilities had 49% of malaria service tracer items.
Challenges within the private sector include sale of unregulated malaria medicines including monotherapies, despite a ministerial ban on monotherapies.  This continues to thrive due to lack of policy enforcement. The NMCP is engaging the private sector in malaria trainings to improve practices in the private sector.  Supply chain management is challenged by delayed procurement processes, weak distribution systems, and lack of accurate consumption data on malaria. 
Several partners operate in South Sudan. The USAID and UNICEF cover the cost for the continuous distribution of LLINs. UNICEF, USAID, DFID, and other humanitarian partners have also supported buying ACTs and artesunate injections for malaria case management through the health cluster.  Population Services International (PSI), Malaria Consortium (MC), Doctors with Africa, Collegio Universitario Aspiranti Medici Missionari (CUAMM), and Health Link South Sudan (HLSS), have been implementing iCCM through a grant from DFID.  Despite the support from partners, partner coordination is weak and challenging due to multiple partners reporting to multiple donors.