South Sudan: “They killed them while we were running”
Warring parties are attacking civilians and destroying medical facilities in South Sudan, leaving more than 700,000 people without access to medical care.
Since early 2025, fighting has intensified across South Sudan in a multi-party war with shifting allegiances along ethnic, regional and political lines.
Doctors Without Borders/Médecins Sans Frontières (MSF) has issued an in-depth report on the impact of violence against civilians in this conflict, “They killed them while we were running.” Indiscriminate attacks on civilians and civilian structures — including bombing hospitals — as well as forced recruitment, sexual violence and constraints on humanitarian aid are now the reality for people in many areas.
The report details 12 attacks on MSF staff and facilities that left an estimated 762,000 people without the access to healthcare between January 2025 and April 2026.
MSF calls on all parties to the conflict to protect and respect civilians and civilian infrastructure.
“They killed them while we were running”
Escalating violence in South Sudan
Constant attacks on civilian areas undermine access to care
The conflict in South Sudan pits government forces, the South Sudan People’s Defence Forces and their allies — including the Uganda People’s defence forces — against a fragmented coalition of opposition groups, including the Sudan People’s Liberation Army – In Opposition (SPLA-IO), the National Salvation Front, the Nuer White Army and allied militias.
Under international humanitarian law, all parties have an obligation to respect and protect civilians and to avoid the use of indiscriminate or disproportionate force, including the use of airstrikes and incendiary weapons in populated areas. Civilians and civilian infrastructure, including healthcare, must never be targeted; direct attacks against them constitute serious violations of international humanitarian law.
“Across these areas, civilians are facing airstrikes and ground attacks, forced recruitment, abductions and widespread sexual and gender-based violence.”
Zakaria Mwatia, MSF country director in South Sudan
“I ran away with my child. I could see the village burning from afar,” says a woman who was displaced and treated at an MSF facility in Chuil, Jonglei state. “They set houses on fire. They burned my grandmother inside the tukul [house]. The elderly stayed behind, they could not run with us. They killed the elders.”
Both targeted and indiscriminate attacks conducted by armed actors are increasingly harming people and undermining access to critical care. Since January 2025, MSF treated an average of 16 people per day for violence-related injuries, across six states — Jonglei, Upper Nile, Central Equatoria, Lakes, Warrap and Western Equatoria — and two administrative areas, Abyei and Greater Pibor.
“Across these areas, civilians are facing airstrikes and ground attacks, forced recruitment, abductions and widespread sexual and gender-based violence,” says Zakaria Mwatia, MSF country director in South Sudan. “Populated towns and villages are being hit, resulting in civilian casualties, mass displacement and the destruction of civilian infrastructure.”
Sexual violence is increasing
In 2025, there were 138 airstrikes in South Sudan, compared to only two in 2024. The impact of violence is evident in MSF’s medical data. In 2025, MSF treated 6,095 people for violence-related injuries, including gunshot wounds, blast injuries and sexual violence, compared to 4,765 people in 2024. Treatment of gunshot wounds alone increased by 77 per cent compared to 2024. From January to April 2026, MSF already treated over 1,800 people wounded by violence, including 885 survivors of sexual violence, highlighting the accelerating toll on civilians.
One patient came to the Yei Civil hospital in Central Equatoria state in March 2026 after being raped by a group of men in Yei. “She did not know by how many,” says
an MSF staff member at the hospital. “She came to us for treatment. After the treatment, her grandmother took her to the village, as she thought she would be safe there. On the next Monday, she went to collect firewood alone. Then, she was raped again by an unidentified armed man. She was back to our clinic on Tuesday.”
South Sudan, 2026. © Isaac Buay/MSF
Healthcare facilities have been targeted
Healthcare has not been spared. Since January 2025, MSF has experienced 12 attacks on our staff and health facilities, including abductions and looting. The MSF-supported hospital in Old Fangak was deliberately bombed by the government forces in May 2025. MSF’s Lankien hospital was also bombarded by the same forces in February 2026. Facilities in Ulang, Pieri and Akobo were looted in separate incidents by unknown assailants. At the same time, humanitarian space is shrinking to an alarming degree.
“General insecurity, access denials and the instrumentalization of aid are increasingly preventing humanitarian organizations from reaching people with the greatest needs,” says Mwatia. “MSF has observed a troubling pattern of access blockages and evacuation orders directed at civilians and humanitarian actors.”
MSF reiterates that civilians, healthcare workers and humanitarian organizations must be protected at all times.
Humanitarian assistance is also being used as a tool for military and political objectives by all parties to the conflict. Attempts to force nongovernmental organizations to relocate aid in certain areas are depriving entire communities — particularly in opposition-held areas in Jonglei and Upper Nile — of vital assistance and preventing an adequate humanitarian response.
Civilians also suffer from forced displacement, immediate and long-term physical harm, increased risk of malnutrition and disease, heightened mental health needs and diminished livelihoods. Harsh living conditions and the long journeys people make without consistent access to food and water have increased their vulnerability, especially when combined with a limited humanitarian response and disrupted essential nutrition supplies.
MSF reiterates that civilians, healthcare workers and humanitarian organizations must be protected at all times and humanitarian access must be unhindered so assistance can reach all people in need, wherever they are.
MSF has been present in South Sudan since 1983 and it remains one of MSF’s largest countries of operations globally.
