Kenya’s healthcare system is on the verge of a major crisis after a sudden drop in foreign aid created a Sh34.7 billion funding shortfall, threatening the availability of essential medicines and services.
The gap, mainly caused by the US government pulling its support, exposes the vulnerability of the country’s heavy reliance on donor funding for health programmes.
A recent study by the University of Nairobi’s Centre for Epidemiological Modelling and Analysis (CEMA) highlights the wide-reaching effects of the aid withdrawal.
Titled Immediate Impact of External Funding Withdrawal on Kenya’s Health Sector, the report examines the flow of external funds into the health system and identifies critical areas at risk, including health service delivery, supply chains, workforce capacity, and equitable access to care.
Kenya’s healthcare is funded through government allocations, private sector contributions, and external aid. In 2018/19, donors provided 18 per cent of total health financing, with the United States contributing over 60 per cent.
This dependence, according to the report, leaves the sector exposed to sudden shocks when aid is reduced or withdrawn.
David Khaoya, lead author and senior research fellow at CEMA, said, “External funding has long played a significant role in Kenya’s health sector, but it is unpredictable and unsustainable. This funding shock is a wake-up call. While the challenges are significant, Kenya and other African countries now have an opportunity to rethink how health systems are financed and build long-term resilience. Increasing domestic investment, strengthening national ownership, and reducing overreliance on external aid are essential if we are to protect health outcomes in the future.”
The report notes a dramatic decline in external funding from Sh126 billion in 2024/25 to Sh54 billion in 2025/26, following the US withdrawal.
Funding for reproductive, maternal, neonatal, and child health (RMNCH) programmes increased to Sh5.85 billion from Sh1.04 billion, but government support fell from Sh1.04 billion to Sh0.54 billion, creating a gap in coverage.
HIV, TB, and malaria programmes are also facing steep reductions. The Global Fund’s support for TB dropped from Sh4 billion to Sh1.74 billion, while malaria funding fell from Sh4.25 billion to Sh1.53 billion. These reductions widened the total commodity gap to Sh34.655 billion, raising concerns about treatment continuity.
Counties will need Sh47.8 billion to retain 41,170 PEPFAR-supported staff, mostly in high HIV-prevalence areas. Without adequate funding, health facilities risk losing critical staff and services, particularly for vulnerable populations such as children, pregnant women, adolescents, and young women.
The study warns that health information systems, which rely heavily on donor support, are under threat. Multilateral funders including the Global Fund, World Bank, WHO, and GAVI may need to reprioritize their programmes in Kenya due to constraints caused by US aid cuts.
Winnie Byanyima, Executive Director of UNAIDS, said, “The funding crisis has exposed the fragility of the progress we fought so hard to achieve. Behind every data point in this report are people, babies and children missed for HIV screening or early HIV diagnosis, young women cut off from prevention support, and communities suddenly left without services and care.”
Kenya faces a high disease burden amid these funding challenges. About 1.4 million people live with HIV, with adult prevalence at 4.9 per cent. Around 140,000 new TB cases are recorded yearly, causing roughly 23,000 deaths. Malaria remains widespread, with 3.5 million cases annually and 70 per cent of the population at risk.
The report identifies five major funding gaps. HIV medicines are short by Sh14.47 billion, risking treatment interruption and drug resistance. TB drugs face a deficit of Sh13.81 billion, which could lead to higher death rates and resistant infections. Childhood vaccines are underfunded by Sh3.09 billion, threatening protection against diseases including polio, measles, pneumonia, and diarrhoea. Malaria prevention and treatment supplies face a shortfall of Sh410 million.
Patrick Amoth, Health Director General, said, “Vaccination campaigns are more than a health intervention; it’s a bold commitment to our children’s future and a shared investment in Kenya’s prosperity.”
Although Kenya’s 2025/26 health budget increased to Sh138.1 billion, an 8.7 per cent rise from the previous year, it still falls below the Abuja Declaration target of allocating 15 per cent of the national budget to health.
“The current domestic budget response in the financial year 2025/26 is not sufficient to bridge the gaps created by donor withdrawal, raising immediate risks for service continuity and longer-term risks for health outcomes and financial protection,” the report notes.
A long-term analysis of the consequences of external funding withdrawal is ongoing and will be published in due course.
