South Sudan

In response to these escalating crises, MSF remained at the forefront of emergency and medical interventions across South Sudan, providing lifesaving healthcare, vaccinations, water and sanitation services, and distributions of essential relief items.

In 2025, our teams provided medical services in two administrative areas and six of the country’s 10 states. In addition to regular projects, MSF opened 12 emergency projects in response to violence, cholera, malaria peaks, flooding and displacement.

Malaria remains the leading cause of morbidity and mortality in South Sudan, accounting for 30–50 per cent of deaths, according to the World Health Organization (WHO), particularly among children under five and pregnant and lactating women. In 2024, there were 3.8 million cases across the country, with annual peaks during the rainy season. Diagnostics, treatment and prevention methods are frequently missing or inconsistently applied. MSF teams continued to treat hundreds of thousands of patients, providing care to more than 200,000 people in 2025, despite rising insecurity and people’s reduced access to health services.

Medical staff is preparing the malaria vaccine

MSF South Sudan Operational Map Explorer

Select a region or project to view local activities, data, and 2025 highlights.

South Sudan Operations

Emergency Responses · 2025

In 2025, MSF responded to conflict, food insecurity, disease outbreaks, and extreme weather with lifesaving medical care and advocacy.

540,300Outpatient consultations

66,873Patients hospitalised

202,856Patients treated for malaria

107,688Children treated for severe malnutrition

20,058Patients treated for cholera

12,191Surgical interventions

Emergency Projects Regular Projects

Abyei Special Administrative Area

MSF provided critical healthcare, including the only surgical care in the area, amid violence and displacement.

24/7Emergency room operations

1,414Cholera cases treated

SurgeryOnly surgical care provider

OutreachIntegrated community case management

Hospital Support

Central Equatoria State

MSF operated emergency and maternity care in Kajo-Keji, and supported Yei civil hospital after a security suspension.

Kajo-KejiEmergency, surgical, & maternity care

Yei TownPrimary healthcare & remote support

SuspensionActivities paused due to insecurity

Yei Civil HospitalMaternity & surgical capacity enhanced

Primary Care Emergency Care

Greater Pibor Administrative Area

MSF reached semi-nomadic populations in Boma and Maruwa with essential healthcare and WASH services.

1,167Patients treated for cholera

4Boreholes drilled for safe drinking water

OutreachCare for semi-nomadic populations

WASHEnvironmental health & hygiene education

Remote Healthcare WASH Interventions

Jonglei State

MSF responded to severe flooding, cholera, and airstrikes, relocating activities from Old Fangak to Paguir and Toch.

860Cholera cases treated before Old Fangak closure

220+Violence-related injuries treated in Old Fangak

RelocationActivities moved to Paguir and Toch

AirstrikesImpacted facilities in Pieri and Lankien

Emergency Response Secondary Care

Northern Bahr El Ghazal State

In Aweil, MSF supported the state hospital with comprehensive care and managed hepatitis E and cholera outbreaks.

SurgerySurgical & post-operative care provided

NutritionInpatient therapeutic feeding centre

OutbreaksHepatitis E & cholera responses

MalariaSeasonal chemoprevention implemented

Hospital Support

Unity State

MSF transitioned from the PoC site to Bentiu state hospital, and mounted flood and cholera responses in Leer.

~7,000Cholera cases seen in Bentiu

3,240Cholera patients hospitalised in Bentiu

300Families received relief items in Yang Payam

45-BedDisease isolation centre planned for Bentiu

Hospital Transition Flood Response

Upper Nile State

MSF delivered care in Malakal, Renk (refugee response), and Ulang, where the hospital was looted and closed.

600+Cholera cases treated in Malakal

500Cholera patients treated in Renk

58,000Refugees/returnees supported in Jerbana & Atam

150,000People left without care after Ulang hospital closure

Refugee Response Ulang Hospital Closed

Warrap State

In Twic county, MSF delivered primary and secondary care through fixed facilities and community-based programs.

HealthcarePrimary & secondary services provided

ReferralsFocus on paediatric & violence cases

MCHMaternal & child healthcare delivered

CommunityDecentralised community-based services

Primary & Secondary Care

Western Equatoria State

In Yambio, MSF ran a short-term paediatric intervention during peak malaria season, with staff training and WASH upgrades.

MalariaSupport during peak malaria season

CapacityTraining for Ministry of Health staff

WASHHospital water supply rehabilitated

PreventionMosquito nets provided for admissions

Short-term Intervention

MSF has been providing essential services including basic healthcare, mental healthcare and specialised medical care to people in the region that is now South Sudan for more than 40 years. Our mobile teams also provide health assistance to displaced people and remote communities. In addition to responding to emergencies and disease outbreaks, we also carry out preventive activities, such as vaccination campaigns and seasonal malaria chemoprevention, as well as distributing safe drinking water and essential relief items. In 2025, our teams treated over 500,000 people in outpatient consultations and over 90,000 patients who needed hospital care.

Our activities in 2025 in South Sudan

South Sudan 2025

Responding to Malaria

30–50%

Of all deaths in South Sudan are caused by malaria (WHO)

3.8 Million

Cases reported nationwide during the 2024 peaks

200,000+

People provided with care by MSF teams in 2025

Malaria remains the leading cause of morbidity and mortality in South Sudan, particularly among children under five and pregnant and lactating women. Diagnostics, treatment and prevention methods are frequently missing or inconsistently applied.

Despite rising insecurity and people’s reduced access to health services, MSF teams continued to treat hundreds of thousands of patients.

Between January and September 2025, MSF treated over 116,100 uncomplicated malaria cases (those which can be treated in the community or in primary care facilities). Patients often travel long distances due to a lack of local facilities, medication or staff, and some primary care facilities refer patients to MSF because they lack...

Attacks on healthcare: a rising threat to lives and medical services

South Sudan 2025

Attacks on Healthcare

9

Attacks on MSF staff and facilities took place in 2025

410,000

People left without care across Ulang, Old Fangak, Yei, and Morobo

1,000+

Chronic disease patients lost access to treatment, including for HIV and TB

The closure of health activities due to attacks and insecurity has disastrous consequences for communities with already limited access to healthcare.

The closure of Ulang hospital left 150,000 people without care. Old Fangak hospital was the only functional facility for over 110,000 people living in remote, flood-prone areas with limited access to medical care. The suspension of activities in Yei and Morobo left 150,000 people without access to essential services between August and November 2025. From November 2025, MSF resumed the provision of emergency and maternity support to the Yei civil hospital, but outreach activities – a lifeline for communities living in remote areas – did not resume.

In Ulang and Old Fangak, MSF teams lost access to over 1,000 patients with chronic diseases, including patients with HIV/AIDS and tuberculosis (TB). In Old Fangak, violence and flooding forced widespread displacement, and by October, 500 out of 638 HIV patients could no longer be accounted for, while others had died.

Responding to infectious disease outbreaks

Between October 2024 and October 2025, MSF responded to cholera in all of its projects, and opened additional emergency interventions, including in Juba, treating over 35,000 patients across nine states – over one-third of all cases reported nationally. A specialised cholera treatment unit was opened at Renk county hospital, treating 500 patients by August, while 1,414 cases were treated in Abyei in 2025. In Pibor, we treated 1,167 patients for cholera. The rapid spread of infectious diseases was driven by population movement – including displacement due to violence – as well as limited surge capacity and chronically under-resourced WASH services.

By November 2024, cholera had reached Malakal, in Upper Nile state, a major transit point for new arrivals from Sudan. MSF teams ran two treatment centres in Malakal county, treating over 600 patients between November 2024 and February 2025. In Bentiu, MSF set up a number of oral rehydration sites and operated 250 cholera beds across its specialised treatment centre in the IDP camp and the Ministry of Health’s Bentiu state hospital until August. This period saw almost 7,000 cases, with 3,240 patients hospitalised.

South Sudan’s WASH sector is chronically underinvested, with recent funding cuts exacerbating the situation. In Bentiu IDP camp and informal displacement sites around Bentiu town, which host thousands of people, the combination of devastating floods in 2021, the influx of refugees from Sudan since 2023, and reduced funding for essential WASH services have contributed to a worsening situation. Fangak county, affected by severe flooding in 2024 and 2025, lacked latrines and clean water; people were forced to drink contaminated floodwater shared with animals.

By the end of June 2025, MSF’s cholera response was ongoing in several key locations including Bentiu, Lankien, Pieri and Abyei. Collaborative efforts to improve access to clean water and WASH facilities are vital to reduce the spread of cholera and prevent outbreaks in the future. Additionally, strengthening healthcare infrastructure, enhancing disease surveillance and response systems, and providing timely access to cholera vaccines can significantly mitigate risks.

Looking Ahead

msf.or.ke

MSF and Ministry of Health teams at Bentiu state hospital will set up a dedicated multi-purpose 45-bed disease outbreak isolation centre for cholera, measles and meningitis. MSF will also launch the MSF Academy for Healthcare with a commitment to strengthen the competencies of Ministry of Health frontline healthcare workers and improve the quality of care provided to patients.

CLICK HERE TO READ THE FULL REPORT

Entrance to Bentiu State Hospital, the main referral facility serving Unity State

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