South Sudanese refugees in Ethiopia’s Gambella region collecting water from a contaminated source, highlighting the lack of sanitation and clean water access in the area.
Refugee, migration and displacement

Left behind in crisis: Escalating violence and healthcare collapse in South Sudan

Article22 December 2025

Doctors Without Borders/Médecins Sans Frontières (MSF) ’ (MSF) report, Left behind in crisis: Escalating violence and healthcare collapse in South Sudan, documents the persistent and worsening barriers to healthcare, at a time when the humanitarian situation in South Sudan is deteriorating. Preventable deaths—especially among women and children—are becoming dangerously normalised. The report is informed by MSF witnessing, routine medical data and testimonies from individuals and staff living in areas where MSF operates. Case studies on malaria, cholera and the Sudan crisis highlight overlapping crises across the country, rooted in chronic gaps in health and basic services. 

Left behind in crisis: Escalating violence and healthcare collapse in South Sudan pdf — 4.48 MB

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Executive summary

In 2025, South Sudan saw a sharp escalation in political tension, violence and insecurity, worsening an already severe situation marked by extremely limited access to healthcare and services. Clashes between government and opposition forces, and non-state armed groups, particularly in Upper Nile, Jonglei, Unity, Central Equatoria and Warrap states, involved attacks on civilians on a scale not seen since the revitalised peace agreement was signed in 2018. This comes at a time when international interest and support are already declining.

MSF has been working in what is now South Sudan since 1983, and the country remains one of the organisation’s largest operations. Present across six states and two administrative areas, MSF fills critical gaps in healthcare services. In 2024, teams treated over 800,000 people in outpatient consultations and 84,800 patients who needed hospitalisation.

Health services in South Sudan are stretched to breaking point

 In all the locations in which MSF works, teams are confronted with the devasting impact on communities of a chronically underfunded health system. Many primary care facilities are non-functional with frequent stockouts of essential drugs, including malaria treatment, and chronic delays in staff payments. Hospitals are neglected, and patients needing life-saving surgery or emergency maternal care have few options. Although gaps in healthcare pre-date the extensive 2025 funding cuts, reduced support has compounded and exposed deep-rooted structural failures, and is likely to exacerbate this trend.

Conflict is driving further gaps in health delivery.

Challenges in delivering health care are even more acute in conflict-affected regions, especially those outside of government control. Many health facilities have closed, staff have fled, and insecurity and access challenges restrict delivery of supplies to the few remaining facilities. More agile humanitarian support is imperative to ensure access to healthcare in these communities.

Targeted attacks on health facilities and staff are increasing.

There has been an extremely concerning increase in attacks on civilians and health facilities by all parties to the conflict, particularly in the Equatorias and Upper Nile. In 2025, MSF alone experienced eight targeted attacks, forcing the closure of two hospitals in Greater Upper Nile and the suspension of primary care activities in Jonglei, Upper Nile and Central Equatoria.

Large parts of the country are experiencing overlapping crises

Conflict, large-scale displacement, flooding and disease outbreaks all contribute to further straining already stretched services. In 2025, in addition to regular projects, MSF opened 12 emergency projects in response to cholera, malaria peaks, flooding and displacement because of violence, compared with five in 2024. These emergencies are interconnected, driven and exacerbated by longstanding gaps in basic services, including health and water, sanitation and hygiene (WASH) services.

Calls to action

The worsening humanitarian crisis in South Sudan needs urgent international prioritisation: populations face overlapping crises, and the current response is failing to meet the rising needs across the country. 

  • International donors to South Sudan must maintain presence and funding commitments; the humanitarian situation is only likely to deteriorate further in 2026. Existing limited funding should be directed to ensure it has a real impact on communities.
  • The protracted nature of humanitarian needs and longstanding challenges in delivering aid should not be used by donors to excuse or normalise the acute gaps in the response that are evident across the country.
  • Funding and investment in health and basic services must be prioritised, as major gaps are having a devastating impact on communities.
  • A scaled-up multisectoral response is essential, including the urgent prioritisation of access to proper and dignified WASH services, due to challenges posed by waterborne diseases.

Shortcomings in existing health projects, including the Health Sector Transformation Project (HSTP), need to be urgently addressed. Despite being overstretched, the HSTP remains a major lifeline for healthcare in much of the country.

  • Donors to the HSTP including WB, UK, Canada, EU, Gavi, the Vaccine Alliance, GF, USA, UAE and others, must honour their funding commitments to the project.
  • Health facilities need support on the ground, not just on paper. The MoH, WB, UNICEF and WHO must ensure the timely delivery of basic drugs and supplies – including for malaria, which continues to be the leading cause of morbidity and mortality – and the payment of staff salaries. Clear and timely communication around funding, supply and staff shortages is needed to ensure continuity of care and coordination with other health organisations.
  • Donors must consider investing in a more comprehensive package of care, including secondary care – currently neglected – particularly for surgery, emergency maternal care and referrals.
  • The Government of South Sudan must scale up its national budget allocations for health, in line with its Abuja Declaration commitment of allocating 15 per cent to health. Budgetary constraints jeopardise efforts to support facilities and ensure the sustainability of healthcare delivery across the country.

At the same time, a shift in approach is also needed to deliver assistance more effectively in South Sudan, especially in conflict-affected areas.

  • In many parts of the country, pre-existing gaps in healthcare delivery are being exacerbated by conflict, insecurity, and access constraints. Despite this, delivery models have not changed.
  • More agile and humanitarian approaches to delivering healthcare are urgently required in these areas, especially in regions not under government control, to ensure all communities have access to care.

Humanitarian access, protection of civilians, and respect for health facilities must be guaranteed across South Sudan.

  • All parties to the conflict, including the SSPDF, SPLA-IO and non-state armed groups, must ensure the protection of health facilities and their staff in line with international humanitarian law (IHL). Safe passage must be guaranteed for medical referrals, the delivery of medical supplies and humanitarian aid, as well as the movement of health and humanitarian staff.
  • All parties to the conflict must ensure the protection of civilians. The use of airstrikes and incendiary weapons in populated areas poses a grave threat to civilians and critical infrastructure. Under IHL, all parties have an obligation to respect and protect civilians and avoid the use of indiscriminate or disproportionate force.
  • Donors, regional actors and the government must reaffirm commitments to humanitarian protection, ensure accountability for attacks on health infrastructure, and enable neutral humanitarian assistance regardless of ethnicity, political affiliation, or location.
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