The post conflict South Sudan has huge challenges in delivering health care to the population. The challenges include: crippled health infrastructures, nearly collapsed public health system, and inadequate qualified health professionals. The country is far from achieving the MDGs by end of 2015. The health system needs a major resuscitation, in addition to supporting and developing health training institutions.
South Sudan is acknowledged to have some of the worst health indicators in the world. [1] [2] [3]
A new measure of expected human capital calculated for 195 countries from 1990 to 2016 and defined for each birth cohort as the expected years lived from age 20 to 64 years and adjusted for educational attainment, learning or education quality, and functional health status was published by The Lancet in September 2018. South Sudan had the second lowest level of expected human capital countries with 2 health, education, and learning-adjusted expected years lived between age 20 and 64 years. This was an improvement over 1990 when its score was 1. [4]
South Sudan's health system is structured into three main service tiers: Primary Health Care Units (PHCUs), Primary Health Care Centres (PHCCs), and hospitals operated at the state, county, police, or military level. [5]
Health service delivery operates across four levels: community, primary, secondary, and tertiary. Community-level services are provided in villages by trained local personnel. The primary level includes PHCUs and PHCCs, which deliver the Basic Package of Health Services (BPHS). The BPHS encompasses preventive, curative, health promotion, and basic administrative services. [6] The government finances it, the Multi-Donor Trust Fund (MDTF), and various NGOs. These services are intended to be free and accessible to the majority of the population at both the primary and secondary levels. [6]
The Ministry of Health (MoH) administers a decentralized healthcare system in line with the Interim Constitution of South Sudan (2005) [7] and the Local Government Act (2009). [6] This system is organized across four administrative levels: national, state, county, and community. [8] The national Ministry is responsible for policy development, strategic leadership, funding, and monitoring and evaluation. State governments oversee the implementation and coordination of healthcare services at the county and community levels.
At independence, the country’s public health system had been severely weakened by prolonged violence and instability, and effective health service coverage remained below 25%. After independence, efforts were made to move away from emergency oriented, health systems largely run by international NGOs toward more sustainable services overseen by the Ministry of Health in South Sudan. Despite these reforms, two years later, international NGOs still provided more than 80% of available healthcare. [9] As of 2022, armed conflict continued to severely reduce access to basic health services for much of the population in South Sudan. The impacts included damage to health facilities, the killing of health workers, widespread malnutrition affecting children, rising mental and psychosocial conditions, and recurrent disease outbreaks and public health emergencies. Despite humanitarian assistance, prolonged conflict continued to erode and exhaust the skilled health workforce, limiting the country’s capacity to deliver care. [10]
In early 2025, health services in South Sudan suffered a major setback following cuts to United States Agency for International Development (USAID) funding initiated under President Donald Trump's "America First" policy. These cuts led to the closure of seven out of 27 Save the Children-supported clinics in Jonglei State and forced 20 others to reduce services, resulting in the layoff of roughly 200 health workers. In April 2025, Save the Children reported that five children were among eight people who died after walking for hours in extreme heat to reach medical care for cholera. A US-funded patient transport service had also been shut down. USAID had previously supported critical interventions for cholera, malnutrition, malaria, and HIV/AIDS, but over 90% of its contracts were reportedly canceled. While the US State Department maintained that some humanitarian projects were still active, it cited widespread corruption in South Sudan’s government as a barrier to continued support. [11]
Apart from the United States, other major donors to South Sudan have already reduced funding or indicated that cuts are forthcoming. In the second half of 2024, the UK announced significant reductions, and the Swedish government shut its Cooperation Office in South Sudan. In response, international organizations have withheld funds to preserve their own viability, further constraining national actors working on the front lines. [12]
The health situation in South Sudan is far from ideal. More than 50% of the population lives below the poverty line, and the adult literacy rate is 27%. The under-five mortality rate (U5MR) is 99 per 1,000 live births, while the broader under-five infant mortality rate is estimated at 135.3 per 1,000. Maternal mortality is the highest in the world, with a Maternal Mortality Ratio (MMR) of 2,053.90 per 100,000 live births in 2006 (South Sudan National Bureau of Statistics, 2012). [3]
Access to antenatal care (ANC) is limited, with 47.6% of women attending the first visit and only 17% completing the recommended four visits. [13] The infant mortality rate (IMR) is 64 per 1,000 live births, and national life expectancy is estimated at 55 years. [14]
In 2004, there were only three surgeons serving Southern Sudan, and just three functioning hospitals. In some areas, there was only one doctor per 500,000 people. [1] A child born in South Sudan has a 25% chance of dying before reaching the age of five. Major causes of child mortality include pneumonia, diarrhea, malaria, and malnutrition. [13]
The country also has one of the lowest immunization coverage rates globally. Only 26% of children received all recommended vaccinations in 2010, a slight decline from 27% in 2006. [15] [16]
Most maternal deaths occur during labour, delivery, or the immediate postpartum period. These deaths are largely preventable with adequate infrastructure and the presence of skilled personnel during childbirth.
South Sudan’s human resources for health are significantly below the minimum threshold recommended by the WHO. [17] Between 2009 and 2010, there were only 189 doctors across eight states—an average of one doctor for every 65,574 people. The number of midwives was 309, or one per 39,088 population. [18] However, estimates vary; other sources suggest a ratio of one midwife per 125,000 women. [19]
In October 2014 Oxfam warned that 2.2 million people were facing starvation. [20] The 2017 South Sudan famine occurred after several years of food insecurity and affected an estimated five million people, just under half the national population. [21] [22]
In 2025, food security improved in some conflict free areas due to better harvests and sustained humanitarian assistance, highlighting the role of stability. However, 7.7 million people, or 57% of South Sudan’s population, continued to face acute food insecurity, with conflict remaining the main driver. Malnutrition also worsened, with 2.3 million children at risk of acute malnutrition, amid access constraints, health service disruptions, and a cholera outbreak affecting Upper Nile and Unity states. [23]
In June 2025, conflict in Upper Nile State, including fighting along the Nile River, [24] sharply worsened food security conditions in South Sudan, placing two counties, Nasir and Ulang, at risk of famine in a worst case scenario. Fighting that escalated from March led to widespread displacement, destroyed livelihoods, and severely restricted humanitarian access. According to the latest IPC analysis, people in 11 of Upper Nile’s 13 counties faced emergency levels of hunger, with around 32,000 people in catastrophic conditions, more than triple earlier projections. Overall, 66% of the state’s population was experiencing crisis, emergency, or catastrophic food insecurity. [23]
The country has a high burden of both communicable (such as malaria, tuberculosis, HIV/AIDS) and non-communicable disease (NCDs). The latter was estimated to have caused 28% of deaths in 2019. [25]
Cholera is mainly transmitted through polluted water and can cause sudden, severe diarrhoea that leads to rapid dehydration and death without treatment. [26] The disease worsens malnutrition by draining the body of essential nutrients. This further weakens patients and creates a cycle in which malnutrition slows recovery and heightens the risk of prolonged illness. [26] Cholera has been a recurring public health problem in Sudan, with outbreaks fuelled by conflict, deficient water, sanitation, and hygiene, [26] and a poorly resourced healthcare system. [27]
South Sudan experienced five cholera outbreaks between 2014 and 2023. These varied widely in scale, with reported case numbers ranging from 424 to 20,038 and fatalities from 1 to 436. Over this period, the case fatality rate ranged between 0.14% and 2.6%. The largest outbreak lasted 14 months, from June 2016 to August 2017, and resulted in a national attack rate of 1.8 per 1,000 inhabitants. After the 2017 outbreak, no community transmission was reported until 2022. The two subsequent outbreaks were limited to single counties, affecting Rubkona in 2022 and Malakal in 2023. [28]
Flooding and conflict driven displacement has increased population movement, which has helped spread cholera within and between counties. Overcrowding in camps or temporary settlements, combined with limited health services, has worsened transmission. In many areas, especially camp like settings, inadequate access to safe water and improved sanitation forces reliance on unsafe sources and contributes to open defecation, further amplifying cholera spread. [28]
The most recent and ongoing outbreak cholera outbreak began on October 2024 in Renk County near the border with Sudan, with initial cases detected among returning citizens and refugees. By January 2025, reports indicated 22,628 cases across 33 of the 80 counties, affecting 7 states and 1 administrative area, many of them located along the Nile. The majority of infections, 84%, are limited to six counties, with Rubkona representing nearly 50% of the nationwide burden. The outbreak has primarily affected children and young adults. More than 50% of reported cases occurred in children under 15 years, including 30% in children under 5 years. Infection rates were similar among men and women. [28] By October 2025, this outbreak had become the worst in the history of South Sudan, with in 95,450 reported cases and 1,587 deaths, corresponding to a case fatality rate of 1.7%. [29] [30]
The funding cuts by USAID starting in 2025 weakened the cholera response during the ongoing epidemic. It lead to disrupted surveillance, rationing of treatment, and the loss of essential services in affected communities. According to humanitarian and former US officials, these reductions coincided with a reversal of declining case trends and contributed to a renewed surge in cholera cases and preventable deaths. [31]
South Sudan experiences malaria transmission throughout the year across all regions, and the disease remains a major cause of illness and mortality among children under five years of age. [32] As in other countries in the East African region, malaria transmission showed strong seasonal variation, with incidence rising sharply during the rainy seasons. [33]
As of 2013, South Sudan had one of the highest malaria burdens in sub-Saharan Africa, with malaria remaining endemic in all 10 administrative states through 2012. Although the Ministry of Health had improved coordination of malaria control and secured major external funding, the disease continued to cause widespread illness and death. [9] In 2016, malaria was the leading cause of morbidity in the country, accounting for 69% of all reported cases of illness. [34] Malaria has continued to pose a major public health challenge in South Sudan, with an estimated 3 million cases reported in 2021 and 7,344 associated deaths. [25] As of November 2025, malaria transmission remained a major challenge for public health. [35]
Malaria control efforts are undermined by large scale displacement, including refugees, returnees, and internally displaced people, as well as natural disasters such as flooding. These pressures further strain a health system weakened by years of conflict and risk reversing gains that have already been made. [9] Renewed fighting in 2016 disrupted malaria control by halting programme activities, restricting or destroying access to health facilities, and worsening shortages of antimalarial medicines. Although the programme later recovered, persistent challenges continue to create gaps in malaria prevention and treatment. [33]
HIV is a retrovirus that attacks the immune system. [36] If untreated, HIV can progress to AIDS. HIV is transmitted through the bodily fluids of an infected person, including blood, breast milk, semen, and vaginal fluids, and can also be passed from a mother to her child. [37]
In 2011, HIV/AIDS was the leading cause of death with almost 120 deaths per 100,000 population; by 2021, the number had fallen to 67. [38] In 2021, mortality was higher among women than men, at 85.4 and 67 deaths per 100,000 population, respectively. [39]
In 2018, only 24% of people living with HIV were aware of their status, and just 16% were receiving treatment. [40] That year, the HIV epidemic in South Sudan was classified as low and generalized, at 2.7 percent, with pockets of higher prevalence of 5 percent or more among high-risk populations. The epidemic was highly uneven across regions and was geographically concentrated in the southern states of the greater Equatorial region.That year, clients of sex workers were linked to roughly 42% of newly recorded HIV cases, while men and women engaged in casual sexual relationships represented about 14.5%. Female sex workers accounted for 11.2% of new cases, and mother-to-child transmission was responsible for approximately 15.7%. [41]
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