South Sudan: Conflict in Jonglei State - Flash Update No. 2 (as of 27 January 2026)

HIGHLIGHTS

• The humanitarian situation in central and northern Jonglei State is rapidly deteriorating amid escalating conflict, widespread displacement and shrinking humanitarian space.

• More than 230,000 people were displaced in Jonglei State by renewed fighting and airstrikes in Nyirol, Uror, Akobo, and Duk counties since 29 December 2025, according to the RRC.

• On 27 January, the DSRSG/RC/HC in South Sudan Ms. Anita Kiki Gbeho chaired the Humanitarian Coordination Forum with the Humanitarian Affairs Minister, Hon. Albino Akol Atak and other Government and humanitarian partners in Juba to agree on urgent measures to improve access and scale up assistance to all people affected by conflict in Jonglei State.

• Flight restrictions have cut off humanitarian air access, halting medical evacuations and delaying life-saving assistance to vulnerable communities.

• On 22 January, the Emergency Relief Coordinator has approved an allocation of $10 million from the Central Emergency Response Fund to address urgent and life-saving needs triggered by escalating violence in Jonglei State.

SITUATION OVERVIEW

The humanitarian situation in Jonglei State, particularly in Nyirol, Uror, Ayod and Duk counties, continues to deteriorate amid escalating conflict, displacement and increasing access constraints. As of 26 January, security conditions in northern and central Jonglei remain volatile, with continued clashes between the South Sudan People’s Defence Forces (SSPDF) and the Sudan People’s Liberation Army in Opposition (SPLA-iO), as well as reported aerial bombardment. Insecurity is significantly affecting civilians and disrupting humanitarian operations, with heightened risks for affected communities and aid workers.

On 25 January, heavy fighting was reported in Biey Boma, Wau Payam, Ayod County, between SSPDF and SPLA-iO. Hostilities reportedly subsided later in the day, although both sides were reported to be regrouping and mobilizing, and further clashes remain possible, including in areas near Ayod Town. On 18 January, authorities reported the arrival of nearly 3,000 displaced people from Duk County to Panyagor Town, Twic East County, reportedly fleeing due to fears of armed attacks. The number of new arrivals has continued to increase.

Between 16 and 19 January, fighting and airstrikes were reported in Tiam Payam (Uror County), Maat Town and Wunlit Payam (Canal/Pigi County), and Pajut Town (Duk County), resulting in casualties and further displacement. Population movements from these areas were reported toward Poktap Town, Duk County, triggering onward displacement toward Twic East County as communities feared the spread of violence. In Pajut, reports indicate damage to civilian homes, loss of property and civilian casualties, with families fleeing with limited belongings.

Humanitarian conditions for displaced populations are worsening. Many people are sheltering in open areas or makeshift structures with limited access to food, health services, and protection, while host communities are under increasing strain. Shelter conditions remain inadequate, exposing vulnerable groups to weather-related risks.

Access constraints continue to impede humanitarian response. Flight restrictions are preventing medical evacuations, the delivery of critical health and nutrition supplies, and staff rotations. Additional limitations on road and river movements, combined with interference in humanitarian operations including reported looting and damage to health and nutrition facilities, confiscation of vehicles and equipment, and intimidation of aid workers, are further restricting the ability of partners to deliver assistance. The United Nations and humanitarian partners continue to call on all parties to respect International Humanitarian Law, ensure the protection of civilians, and facilitate safe, timely and unhindered humanitarian access.

HUMANITARIAN IMPACT AND NEEDS

As of 26 January, 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). Displacement includes 105,400 people in Uror, 57,200 in Nyirol, 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 strain on host communities and basic services. Access to several displacement-affected areas remains constrained. In addition, local authorities have registered over 26,500 arrivals from Jonglei in Mingkaman, Awerial County (Lakes State).

On 25 January, Government forces ordered the evacuation of civilians and all United Nations and humanitarian personnel from Nyirol, Uror and Akobo counties within 48 hours, citing an impending military operation against SPLA-iO forces.

Health service delivery has been significantly disrupted. Health facilities in Waat and Riang (Nyirol County) and Yuai and Kaljak (Uror County) were reportedly looted. or vandalized, resulting in service suspension and staff displacement. As a result, an estimated 115,000 people have lost access to basic health care. At least three health facilities and 24 nutrition sites providing life-saving services were looted or forced to close, interrupting treatment for approximately 8,000 children and 3,000 pregnant and breastfeeding women.

According to local health authorities, cholera cases are rapidly increasing in Duk County, with 938 cases and 29 deaths reported as of 25 January. Transmission remains active in IDP-hosting areas, driven by overcrowding and critical gaps in safe water, sanitation and health services. Health facilities are overstretched, and urgent support is required to contain the outbreak and prevent further loss of life. On 25 January, a suspected cholera case was reported in Hai Zain, New Fangak (Fangak County); the patient was isolated and treated, and enhanced surveillance and case search were initiated.

Security conditions continue to restrict humanitarian operations. On 24 January, Médecins Sans Frontières (MSF) evacuated critical staff from its health facility in Akobo County following instructions from authorities and due to deteriorating security, reducing services to a minimum. On 25 January, an international NGO also requested the relocation of staff from Akobo amid reports of a potential attack. Between 31 December 2025 and 8 January, 48 aid workers were relocated.

On 21 January, reports of an imminent attack on Ayod Town triggered large-scale civilian displacement to surrounding villages, while shops and businesses were reportedly looted. Locally recruited staff of four international NGOs relocated to Canal, Pajiet and Tuok bomas in northern Jonglei, which are now hosting large numbers of displaced people from Ayod.

On the same day an international NGO reported that security forces entered their compound in Ayod Town and confiscated vehicles, fuel, communications equipment and other assets, prompting humanitarian agencies to relocate their staff from the area.

On 25 January, the Chairperson of the SPLM National Youth League raised concerns over rising starvation risks affecting more than 20,000 displaced people in Duk County, following recent clashes. After the leaders assessment, they indicated severe food and basic service gaps and called for urgent government and humanitarian assistance.

On 25 January, UNMISS expressed grave concern over reports of threats of indiscriminate violence against civilians in Jonglei State, where more than 180,000 people have reportedly been displaced by recent fighting. UNMISS condemned inflammatory rhetoric targeting civilians and urged South Sudan’s leaders to halt hostilities, uphold the ceasefire and their commitments under the peace agreement, and pursue inclusive dialogue to de-escalate the situation.

On 27 January, the Catholic Bishops of the South Sudan Ecclesiastical Province expressed concern over the deteriorating political, security and humanitarian situation, condemning renewed fighting between Government forces, the SPLA-IO and other armed groups, particularly in Jonglei and Eastern Equatoria states. The Bishops called on leaders of the Revitalized Transitional Government of National Unity and non-signatories to the Revitalized Peace Agreement to halt hostilities and pursue dialogue.

Beyond Jonglei, clashes have also been reported in Unity, Eastern Equatoria and Central Equatoria states, further straining humanitarian capacity. In Unity State, fighting in Guit, Rubkona and Leer counties displaced an estimated 48,700 people as of 16 January (including 24,500 in Rubkona, 17,000 in Leer, and 7,250 in Guit). In Kapoeta East County (Eastern Equatoria), approximately 2,000 people have been displaced. Humanitarian activities in these areas have been disrupted by insecurity.

HUMANITARIAN RESPONSE AND CHALLENGES

The humanitarian response has been directly affected. Health and nutrition facilities have been destroyed or looted, resulting in the closure of 24 nutrition sites and cutting off life‑saving services for children and pregnant and breastfeeding women. Flight bans of United Nations Humanitarian Air Services (UNHAS), MSF, ICRC and MAF imposed for the first time in several years have severely disrupted humanitarian operations, denying air access to critical locations. Medical evacuations are halted, life-saving supplies are delayed, and staff rotations in high-risk areas are suspended, placing already at-risk communities in even greater danger.

On 22 January, humanitarian partners conducted a low-profile assessment in Baidit IDP site, Taragok, Block 04, Bor Stadium, and Bor IDP camp in Bor Town, Bor South County, identifying 4,390 conflict-displaced people from central and northern Jonglei State. Priority needs include food assistance, shelter and non-food items, WASH support, and health services.

High-level advocacy continues under the leadership of the Humanitarian Coordinator (HC), with the Humanitarian Country Team (HCT) engaging senior Government officials—including the Ministry of Humanitarian Affairs and Disaster Management, the Ministry of Defense, and the Chief of Defense Forces—as well as the diplomatic and donor community to advocate for civilian protection and unhindered humanitarian access.

On 24 January, the DSRSG/RC/HC, Ms. Anita Kiki Gbeho, met with the Minister of Humanitarian Affairs and Disaster Management, Hon. Albino Akol Atak, to review the deteriorating humanitarian situation in Jonglei and agree on further assessments and response actions for the most vulnerable.

On 20 January, the Embassies of Canada, France, Germany, Japan, the Netherlands, Norway, Switzerland, the United Kingdom, and the United States issued a joint statement expressing grave concern over escalating violence in Jonglei, Eastern Equatoria, and other parts of the country, calling for an immediate cessation of hostilities and safe, unhindered humanitarian access.

On 26 January, the UN Commission on Human Rights in South Sudan warned that inflammatory rhetoric by senior military figures and reports of troop mobilization in Jonglei State significantly increase the risk of mass violence against civilians and further undermine the peace agreement. The Commission described recent public statements by commanders—combined with active force mobilization—as a dangerous escalation, citing remarks by a senior military official instructing troops in northern Jonglei to “spare no lives,” including the elderly.

A joint Government–humanitarian partners meeting on the Jonglei conflict was held on 27 January, co-chaired by the Minister of Humanitarian Affairs and Disaster Management and the Humanitarian Coordinator, Ms. Anita Kiki Gbeho. Senior Government officials and humanitarian partners reviewed the deteriorating situation and agreed to scale up immediate assistance in areas assessed as safe, while ensuring a principled response for all affected people, including those in Government- and opposition-controlled areas.

The Government committed to addressing key operational constraints, including bureaucratic impediments and illegal taxation, and to facilitating safe, unimpeded humanitarian access through the Ministry of Defence. Clear guidance will be issued to protect humanitarian personnel and assets, and options for a one-stop mechanism to resolve access challenges will be explored. On 27 January, the Acting HC departed for a high-level mission to Bor Town to engage state authorities on ensuring humanitarian access and support for conflict-affected populations.

FUNDING

On 22 January, the Emergency Relief Coordinator (ERC) approved an allocation of US$10 million from the Central Emergency Response Fund (CERF) to address urgent and life-saving needs resulting from escalating violence in Jonglei State. The allocation will be implemented by five United Nations agencies, in partnership with humanitarian actors, and will directly target 178,000 of the most affected people.

The CERF funding will support the delivery of 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.