Outbreak Alert🌍ReliefWeb – WHO Outbreak Reports
South Sudan Conflict Sparks Cholera Outbreak and Healthcare Crisis in Jonglei State
Executive Summary
Renewed conflict in South Sudan’s Jonglei State has displaced over 276,000 people, exacerbating a severe cholera outbreak and a critical healthcare emergency. Looted medical facilities leave 1.35 million without essential services. Aid efforts face immense challenges from ongoing insecurity, damaged infrastructure, and impending heavy rains, intensifying the urgent need for humanitarian assistance and safe access for vulnerable communities.
The heart of South Sudan's Jonglei State is grappling with a profound humanitarian crisis, ignited by escalating conflict. As of late March 2026, a surge in violence has not only uprooted hundreds of thousands of people but has also dismantled essential services, plunging communities into a desperate struggle for survival. This volatile situation, detailed in recent reports from humanitarian agencies, highlights a critical need for sustained aid and stability.
## Mass Displacement and Daily Struggles for Survival
Since January, the ongoing clashes, primarily between the South Sudan People’s Defence Forces (SSPDF) and the Sudan People’s Liberation Army in Opposition (SPLA-iO), have forced a staggering 276,500 individuals to flee their homes across Jonglei, Lakes, Upper Nile, and Central Equatoria states. This figure represents a significant increase from just a week prior, indicating a rapidly worsening situation. Many have been displaced multiple times, seeking safety wherever they can find it. Adding to this internal displacement, an estimated 110,000 people have crossed the border into neighboring Ethiopia, desperately searching for refuge.
Life for these displaced populations is fraught with peril. Many undertake long, arduous journeys without food or water, arriving at makeshift settlements with little to no shelter, safe drinking water, or proper sanitation. A recent assessment in Akobo Town, following a military takeover, revealed it to be largely deserted, with an estimated 114,000 residents dispersed across numerous remote locations within Akobo County. The sheer scale of displacement strains already scarce resources and places immense pressure on host communities, who often share their meager provisions. Concerns about protection, particularly for women and children, remain incredibly high, with reports of gender-based violence emerging amidst the chaos.
## Healthcare Under Attack: Critical Services Lost
The conflict has inflicted severe damage on South Sudan’s already fragile healthcare infrastructure. According to the World Health Organization (WHO), at least 26 health facilities across six counties—Akobo, Nyirol, Uror, Canal/Pigi, Ayod, and Duk—have been destroyed, looted, or rendered completely non-functional since the conflict escalated in late December 2025. This devastation means that approximately 1.35 million people in Jonglei State have lost access to vital health services, including basic medical care, vaccinations, and emergency treatment.
The looting of facilities has been particularly devastating. Médecins Sans Frontières (MSF), a leading humanitarian medical organization, reported that its hospital and offices in Akobo Town were completely ransacked. This hospital, once a lifeline for over 100,000 people, is now inoperable. Medicines were not only stolen but also deliberately destroyed, and all essential equipment, including 50 hospital beds, was removed. Such systematic destruction prevents any immediate resumption of medical services, denying critical care to those in dire need. Humanitarian organizations are calling for investigations and guarantees of safety before considering any return, emphasizing the deep impact on their ability to deliver aid.
## Escalating Health Crises: Cholera and Malnutrition
Amidst the conflict and displacement, preventable diseases are surging, with cholera posing a significant threat. Cholera is a severe diarrheal disease caused by ingesting contaminated food or water, leading to rapid dehydration and, if untreated, death. The conditions in displacement sites—overcrowding, lack of clean water, and inadequate sanitation—create a perfect breeding ground for its rapid spread. Between March 18 and 24 alone, 155 new cholera cases and two deaths were reported across nine counties, including several in Jonglei State. Since the outbreak began in September 2024, a staggering 100,759 cases and 1,653 deaths have been recorded across 55 counties in nine states and three administrative areas. The outbreak has increasingly shifted its focus to Jonglei and Lakes states, directly linked to the massive population movements and dire hygiene conditions.
Malnutrition is another escalating crisis, particularly affecting the most vulnerable. Humanitarian partners have reported a complete halt of nutrition services in several conflict-affected areas, especially Akobo and Canal/Pigi counties. In southern Canal/Pigi, 12 nutrition sites are now non-functional due to damage and looting. This suspension puts over 4,600 children under five and nearly 3,000 pregnant and breastfeeding women—who were previously receiving treatment—at an even higher risk of severe acute malnutrition (SAM) and moderate acute malnutrition (MAM). The lack of access to nutritious food and therapeutic feeding combines with disease outbreaks to create a vicious cycle, weakening immune systems and increasing mortality rates. In addition to cholera and malnutrition, there are ongoing reports of measles cases in Ayod County, alongside widespread acute health issues like pneumonia and general diarrhea.
## A Coordinated Response Amidst Obstacles
Despite the daunting challenges, humanitarian partners are actively scaling up their response efforts. The UN Humanitarian Coordinator in South Sudan, Ms. Anita Kiki Gbeho, met with the Minister of Humanitarian Affairs and Disaster Management to discuss the worsening situation. Both emphasized the urgent need to facilitate the safe, voluntary, and dignified return of displaced people, especially as the rainy season approaches, which could further complicate movements and aid delivery. The government has affirmed its readiness to coordinate assistance, with the UN reaffirming its commitment to ensuring returnees receive essential services like shelter, water, healthcare, and food.
Various clusters of humanitarian agencies are working together to deliver aid. The Logistics Cluster has facilitated the delivery of 54 metric tons of crucial supplies—including education, nutrition, and protection items—by air and road. The Food Security and Livelihoods Cluster has provided general food assistance to over 113,300 people and cash aid. Organizations like the Food and Agriculture Organization (FAO) are also working on longer-term solutions, such as distributing cool boxes to fish processors to support livelihoods and constructing classrooms for agricultural training.
The Health Cluster, led by WHO, is coordinating responses, providing emergency supplies, and sharing vital information on outbreaks and service disruptions. Médecins Sans Frontières (MSF) is scaling up medical and humanitarian support in places like Chuil, Nyirol County, by upgrading health centers and running mobile clinics. The Water, Sanitation, and Hygiene (WASH) Cluster partners have distributed relief items such as mosquito nets, blankets, soap, and jerry cans to thousands of families. They are also repairing hand pumps, establishing emergency water systems, and constructing latrines to improve access to safe water and sanitation, crucial for preventing cholera and other waterborne diseases. Oral cholera vaccination campaigns are also underway, with over 24,000 people vaccinated in Duk County, but much more is needed to contain the widespread outbreak.
## Roadblocks to Recovery: Major Challenges Ahead
The path to recovery and stability in Jonglei State is fraught with significant challenges. Foremost among these is the pervasive insecurity and active fighting, which continue to impede access for humanitarian workers and disrupt critical services. The military presence and ongoing clashes prevent the safe movement of civilians and aid, leading to staff displacement and a discontinuity of care.
Logistical hurdles are also immense. State-level storage and logistical capacity remain insufficient for pre-positioning large quantities of aid, and existing facilities are often damaged or looted, further limiting the ability to quickly restore full services. Reaching remote, swampy border areas is exceptionally difficult. Road access to many parts of Jonglei, including the critical Walgak–Akobo route, remains unfeasible, forcing expensive reliance on air assets. Moreover, the risk of further looting discourages aid organizations from pre-positioning supplies, leaving communities vulnerable.
The suspension of vital programs, such as the World Food Programme’s operations in Akobo East and West due to military evacuation orders, means that already desperate communities are cut off from essential food assistance. Without a significant improvement in security and unhindered access, the humanitarian situation in Jonglei State is set to worsen, particularly with the onset of the rainy season, which will make many areas impassable and increase the risk of disease transmission and population entrapment.
## A Call for Urgent, Sustained Support
The dire situation in South Sudan's Jonglei State demands immediate and sustained attention. The confluence of conflict, mass displacement, and the collapse of health and sanitation services has created an urgent humanitarian catastrophe. The coordinated efforts of national and international partners are vital, focusing not only on immediate relief but also on rebuilding essential infrastructure and restoring livelihoods. Ultimately, a lasting solution requires an end to the conflict, ensuring peace and security that allows for the safe, voluntary, and dignified return of all displaced people, enabling them to rebuild their lives with access to basic human rights and services.
Key Takeaways
- ✓Conflict in Jonglei State has displaced over 276,500 people internally and 110,000 to Ethiopia, creating urgent needs for food, water, and shelter.
- ✓At least 26 health facilities have been destroyed or looted, leaving 1.35 million people without essential medical care, severely worsening health outcomes.
- ✓A major cholera outbreak is escalating, with over 100,000 cumulative cases, driven by displacement and poor sanitation; urgent WASH and vaccination efforts are critical.
- ✓Ongoing insecurity, widespread looting, and challenging logistics, intensified by impending rains, severely hinder humanitarian access and the delivery of life-saving aid.
- ✓Sustainable peace, secure access for humanitarian efforts, and robust support for safe returns are essential to address the crisis and prevent further suffering.