South Sudan is among the 23 highest burden malaria countries in the world (1% of all global malaria cases and deaths in 2019 ). Between 2016 and 2019, the case burden for malaria fell by 14.5% (from 130 to 111 per 1000 of the population at risk), while deaths fell by 4% (from 0.39 to 0.38 per 1000 of the population at risk.
Malaria is endemic throughout South Sudan and continues to be a major public health problem. Transmission of malaria in South Sudan occurs throughout the year and peaks on rainfall, except in urban cities. South Sudan’s rainy season lasts for about six to eight months (April to November). 
Plasmodium falciparum is the main parasite species and causes up to 93% of all malaria cases with more than half of these occurring as mixed infections with P. malariae. Other plasmodium species present in the country are P. ovale and P. vivax. The malaria parasites are transmitted by vectors Anophelesgambiaess, An. arabiensis and An. Funestus. 
Long Lasting Insecticidal Nets (LLINs) are the main vector control intervention in South Sudan. Indoor Residual Spraying (IRS) is on the other hand implemented on a small scale within a few internally displaced and refugee settings.  South Sudan’s LLIN distribution methodology consciously recognizes the woman as the head of the household. This removes all societal norms and hurdles and thereby make the intervention accessible to the women. 
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. 
Malaria in pregnancy
Protecting pregnant women from malaria is done with ITNs and intermittent preventative treatment of malaria in pregnancy (IPTp) with sulfadoxine pyrimethamine. 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 sulfadoxine-pyrimethamine (SP)/Fansidar® increased from 38% to 67%, while the percentage of women with at least two doses of SP/Fansidar increase from 32% to 57%. 
However, scaling up IPTp to at least 3 doses of sulfadoxine-pyrimethamine (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. 
Malaria diagnosis and treatment
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. 
Supply chain management is challenged by delayed procurement processes, weak distribution systems, and lack of accurate consumption data on malaria. 
Public sector and private sector challenges
Public sector challenges include inadequate trainings, unavailability of job aids at the health facilities and inadequate supportive supervision.  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. 
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 with 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.