South Sudan Launches Major Health Sector Transformation with WHO Partnership

In his remarks at the signing ceremony, Dr. Anin Ngot Mou, Undersecretary at the Ministry of Health, emphasized the transformative nature of the agreement.

In a significant move towards overhauling the national healthcare system, the Ministry of Health (MoH) of South Sudan and the World Health Organization (WHO) have officially signed the Health Systems Strengthening (HSS) output agreement, a vital component of the broader Health Sector Transformation Project (HSTP). This landmark agreement represents a coordinated, government-led initiative aimed at building a stronger, more resilient, and inclusive health system over the next three years.

The HSTP marks a new era in healthcare development in South Sudan, where fragmented and donor-driven health services are being unified under a national approach. This transformation initiative replaces previous major donor-funded programs such as the Health Pooled Fund (HPF), COVID-19 Emergency Response, and the Health Systems Strengthening and Recovery Support Project (CERSSP). The HSTP streamlines efforts to improve healthcare delivery in a country plagued by years of conflict, underdevelopment, and persistent humanitarian crises.

South Sudan’s healthcare system is currently among the most challenged in the world. Decades of conflict have severely undermined infrastructure and public service delivery. The impact has been devastating: WHO estimates that the country has the highest maternal mortality rate globally, with 1,223 deaths per 100,000 live births. Neonatal and child mortality rates remain alarmingly high, at 64 and 99 deaths per 1,000 live births respectively, with little improvement over the past decade.

In his remarks at the signing ceremony, Dr. Anin Ngot Mou, Undersecretary at the Ministry of Health, emphasized the transformative nature of the agreement. “HSTP is a crucial step towards ensuring that health resources are better structured and more sustainable in delivering high-quality healthcare to our people,” said Dr. Mou. “This milestone is historic. It is the first time the Ministry of Health is leading a health transformation project of this scale. We are fully committed to assuming leadership and responsibility, and to working closely with WHO and other partners to reform the health system, enhance governance, expand essential services, and move toward a sustainable future.”

The HSTP is backed by the Health Multi-Donor Trust Fund, with financial contributions totaling USD 12.7 million. The fund is supported by a consortium of international donors, including the World Bank, the United Kingdom’s Foreign, Commonwealth & Development Office (FCDO), Canada, and the European Union, among others.

Dr. Humphrey Karamagi, WHO Representative to South Sudan, described the initiative as a turning point in the country’s healthcare development. “This project presents a unique opportunity to introduce innovations tailored to the South Sudanese context. We’re building a health system that is resilient, adaptable, and inclusive,” said Dr. Karamagi. “The HSTP aligns with the national Health Sector Strategic Plan (HSSP) and is expected to significantly contribute to its core objectives—ensuring equitable access to essential health services, strengthening the health workforce, improving health information systems, and advancing toward Universal Health Coverage.”

WHO’s role in the HSTP includes technical assistance, capacity building, and the introduction of innovative models to enhance service delivery in fragile settings. Its support will complement operational efforts spearheaded by UNICEF and other health sector actors.

The project's implementation comes at a critical time. South Sudan continues to battle multiple overlapping emergencies, including flooding, displacement, outbreaks of infectious diseases, and food insecurity, all of which place additional strain on the healthcare system. These challenges highlight the urgent need for a more robust, coordinated, and resilient health sector.

The HSTP’s strategic approach aims to:

• Strengthen primary health care systems and service delivery across underserved areas.

• Improve maternal, newborn, and child health outcomes through targeted interventions.

• Enhance governance, accountability, and local ownership of health services.

• Build health infrastructure and improve access to essential supplies and equipment.

• Train and deploy more qualified health workers across the country.

• Ensure the integration of humanitarian and development health services, reflecting the country’s complex realities.

The signing ceremony, held under the theme “Together Towards Achieving Better Health Outcomes,” symbolized the government’s dedication to reforming the sector and underscored the importance of collaboration among national and international partners.

The partnership also aligns with global health goals, particularly the Sustainable Development Goal (SDG) 3, which calls for ensuring healthy lives and promoting well-being for all at all ages. The emphasis on local leadership, government accountability, and innovative, context-specific solutions sets the HSTP apart as a pioneering initiative within the region.

As South Sudan embarks on this critical transformation journey, the HSTP is expected to set the foundation for a resilient health system that can better respond to the needs of its people—now and in the years to come.