South Sudan: Conflict in Jonglei State Flash Update No. 3 (as of 30 January 2026)

HIGHLIGHTS

• As of 30 January, the humanitarian situation in Jonglei State continues to deteriorate rapidly due to escalating conflict, which has triggered widespread displacement while severely constraining humanitarian access.
• Families fleeing violence are sheltering in the open, under trees or in makeshift structures, with little or no access to food, health care, or protection services, and are largely dependent on already overstretched host communities.
• An estimated 260,000 people have been displaced across Jonglei State following renewed fighting and airstrikes since 29 December 2025, according to the Relief and Rehabilitation Commission (RRC).
• Cholera transmission in Duk County is increasing sharply, with 982 cumulative cases and 30 deaths reported as of 25 January; treatment centres are overwhelmed and facing critical supply shortages, necessitating an immediate scale-up to a full emergency response.

SITUATION OVERVIEW

As of 30 January, the humanitarian situation in Jonglei State continues to deteriorate rapidly due to escalating conflict, which is driving displacement and severely constraining humanitarian access. The impact of insecurity is compounded by a worsening cholera outbreak, further heightening risks to affected communities. Security conditions in northern and central Jonglei remain volatile, with ongoing clashes between the South Sudan People’s Defence Forces (SSPDF) and the Sudan People’s Liberation Army in Opposition (SPLA-iO), as well as reports of aerial bombardment. Insecurity is increasingly affecting civilians and disrupting humanitarian operations, raising protection concerns and operational risks for aid workers.

On 28 January, clashes broke out in Pathai town, Uror County, as SSPDF forces advanced from Ayod County towards the northern outskirts of Yuai. The fighting followed the movement of SSPDF forces on 27 January amid broader military operations in Uror County. Information on civilian casualties and damage remains limited.

Displaced families are reportedly sheltering in the open, under trees or in makeshift structures, with limited access to food, health services, safe water, and protection, and are largely dependent on already overstretched host communities. Health facilities have been looted or vandalized, leaving an estimated 115,000 people without access to basic health care in Yuai, Nyirol, and Uror. Meanwhile, critical gaps in health services and supplies have been reported across Duk, Canal/Pigi, Akobo, Ayod, and Fangak, affecting a combined catchment population of over one million people, due to conflict and access constraints. On 25 January, Government forces ordered civilians and personnel from the UN and other humanitarian organizations to evacuate Nyirol, Uror, and Akobo counties within 48 hours ahead of a planned military operation.

In Duk County, the Commissioner reported that the security situation remains relatively calm; however, humanitarian needs are rising sharply due to the continued arrival of displaced people from Pajut and Uror, escalating cholera transmission, and acute shortages of food and safe water, with only a limited number of boreholes functioning. Displaced families have reportedly not received food assistance since 2 January due to conflict-related disruptions, while new arrivals continue. The Commissioner also noted that conditions in Pajut remain stable, but destruction from fighting on 16 January has prevented returns, with bodies yet to be retrieved, and requested increased humanitarian support and advocacy.

HUMANITARIAN IMPACT AND NEEDS

More than 230,000 people have been displaced across Jonglei State following renewed fighting and airstrikes since 29 December 2025, according to the Relief and Rehabilitation Commission (RRC). Insecurity and access constraints have prevented needs assessments in most displacement locations. Displacement includes 105,400 people in Uror, 57,200 inNyirol, 27,000 in Duk, 17,000 in Ayod, 11,000 in Akobo, 8,000 in Twic East, and 4,300 in Bor South counties, placing severe pressure on host communities and basic services. Access to several displacement-affected areas remains constrained. In addition, local authorities report over 29,000 arrivals from Jonglei in Mingkaman, Awerial County (Lakes State) as of 28 January.

Population movements beyond Jonglei continue. As of 23 January, approximately 6,000 people, predominantly women and children, had arrived in Mangalla, Juba County (Central Equatoria). While some displaced families are staying with relatives or host communities, others with greater resources have relocated onward to Juba and surrounding areas. On 29 January, authorities reported new displacement from Jonglei into Ulang County (Upper Nile State) and Pigi County (Jonglei State). In Ulang County, over 13,000 IDPs were verified, including 6,097 in Nyangor, 6,750 in Breach, and 240 in Thullp, while approximately 6,000 people were reportedly displaced from Nyirol to Pigi County. The World Food Programme (WFP) is planning to provide food assistance to IDPs in Ulang County.

The displacement crisis is being compounded by a rapidly escalating cholera outbreak, particularly in Duk County. As of 25 January, 982 cholera cases and 30 deaths were reported, with treatment centres overwhelmed and critically short of supplies, indicating the need for an immediate shift to full emergency response. An MSF assessment conducted on 28–29 January found a sharp increase in cases since mid-January, including 48 cases and four deaths reported at Poktap Health Care Centre alone. Displaced populations from neighbouring counties are among the most affected.

There are four cholera treatment centres in Duk County, all facing severe shortages of cholera kits, personal protective equipment (PPE), and infection prevention and control (IPC) materials. At Poktap health facility, a 10-bed cholera treatment centre was accommodating 16 patients, with some patients reportedly treated on the floor. Health workers are reusing IV equipment due to shortages, while WASH support is largely absent. These conditions significantly increase the risk of transmission and mortality.

Counties including Nyirol and Akobo have recorded some of the highest cholera case fatality rates since the start of the outbreak. However, limited or no access to these areas has severely constrained surveillance, raising concerns about undetected outbreaks and preventable deaths. Based on trends observed in Duk County, similar surges are likely occurring in inaccessible areas. Scaling up case management, emergency supplies, surveillance, WASH interventions, and vaccination is urgently required to prevent further escalation. Between 27 and 30 January, the Acting Humanitarian Coordinator and partners visited Bor County to assess the evolving humanitarian, security, and operational context.

HUMANITARIAN RESPONSE AND CHALLENGES

The United Nations and humanitarian partners are scaling up assistance in safer areas, while continuing to advocate for sustained improvements in access. Authorities have reiterated their commitment to address bureaucratic impediments, and the UN and partners continue to call on all parties to facilitate safe, timely, and unhindered humanitarian access to all people in need, in line with international humanitarian law.

On 26 January, an Initial Rapid Needs Assessment (IRNA) was conducted among people displaced from Jonglei State to Mingkaman, Awerial County (Lakes State), where over 29,000 displaced people have been registered. The assessment identified urgent needs for shelter and non-food items, food assistance, nutrition support, health services,protection, and WASH services. Humanitarian partners are mobilizing resources to respond; however, Awerial County is classified as IPC Phase 4 (Emergency) in the 2025 FSNMS analysis, and food insecurity is expected to worsen as limited resources are shared with newly arrived displaced people.

On 28 January, the Humanitarian Coordinator for South Sudan, Ms. Anita Kiki Gbeho, met with the Minister of Interior, Hon. Aleu Ayieny Aleu, to strengthen cooperation on addressing security-related challenges affecting humanitarian operations. The Humanitarian Coordinator reaffirmed the UN’s readiness to support government-led efforts to improve security and enable humanitarian action, while the Minister reiterated the Government’s commitment to close collaboration with the United Nations.

In Duk County, three health facilities, Lost Boys County Hospital, Pajut PHCC, and Koyong PHCC have been removed from the Health Sector Transformation Project (HSTP) due to funding constraints. An international NGO continues to provide nutrition services in Por Chol PHCU, Chol TIM PHCU, and Tiem PHCU, where limited supplies remain available.

Humanitarian partners remain deeply concerned by worsening access constraints in Jonglei State. Escalating hostilities and large-scale displacement continue to impede humanitarian operations, while flight restrictions are preventing medical evacuations, the delivery of critical health and nutrition supplies, and staff rotations. As of 28 January, flight restrictions have affected humanitarian assistance to an estimated 366,000 people in northern and central Jonglei. Conflict has also disrupted road pre-positioning, while additional constraints on road and river access, looting, damage to facilities, confiscation of vehicles and equipment, and intimidation of aid workers further limit partners’ ability to reach people in need. The Access Working Group is developing an access strategy to secure sustained immediate, safe, and unhindered humanitarian access to all affected and high-risk areas, including locations that remain inaccessible.

FUNDING

On 28 January, the Humanitarian Coordinator for South Sudan, Ms. Anita Kiki Gbeho issued a statement welcoming the approval by the Emergency Relief Coordinator (ERC), Mr. Tom Fletcher, of a US$10 million allocation from the Central Emergency Response Fund (CERF) to address urgent, life-saving needs arising from escalating violence in Jonglei State.

The CERF funding will support primary health care, water, sanitation and hygiene (WASH) services, shelter materials and essential non-food items, emergency food assistance through cash-based interventions, and prevention and response services for gender-based violence and violence against children.

The CERF allocation will be complemented by additional resources from the South Sudan Humanitarian Fund (SSHF) to further scale up the response in areas of greatest need. In parallel, the Government reported ongoing efforts to mobilize the private sector to provide approximately six metric tons of food assistance for conflict-affected people in Jonglei State.