Kenya is facing a Sh72 billion shortfall in health funding after a steep drop in donor support, a shift that experts warn could undo years of progress against HIV, tuberculosis and malaria.
New figures from the Centre for Epidemiological Modelling and Analysis (CEMA) at the University of Nairobi show that external health financing fell sharply in the 2025/26 financial year. Total donor support dropped from Sh126 billion the previous year to Sh54 billion.
The decline has come fast. It coincides with the withdrawal of United States government funding, long the single largest backer of Kenya’s health sector.
This has happened even as the Ministry of Health’s overall budget rose slightly to Sh138 billion, up from Sh127 billion in 2024/25. Of that amount, Sh119 billion comes from the government. The rest is a mix of donor money channelled through the ministry, funds routed via the National Treasury, and off-budget support managed directly by partners.
External financing still makes up a large share of health spending. But the scale has shrunk dramatically.
“The annual trend in total external funding was rising before 2025/26,” the CEMA report notes. “That pattern breaks sharply this year, largely due to the withdrawal of US government funding and reduced support from the Global Fund and the World Bank.”
The sharpest fall was in off-budget funding, which dropped from Sh87 billion to Sh26 billion. These funds, often managed outside government systems, have historically been the main route for US support. Their sudden loss has left programmes exposed and given the government little room to redirect resources.
On-budget donor support also fell, from Sh39 billion to Sh28 billion. Cuts from the Global Fund accounted for most of that drop, alongside a smaller reduction from the World Bank.
For decades, Washington underpinned Kenya’s health response, providing more than half of all external health funding on average before 2024/25. That support ended after the United States formally withdrew funding and membership from the World Health Organization in January 2026, following an executive order signed a year earlier. The decision cited concerns over the WHO’s handling of the Covid-19 pandemic and governance issues.
The impact is already being felt. Some immunisation programmes supported through multilateral channels, including those linked to Gavi, have had to reshuffle budgets to keep services running.
CEMA warns that the biggest shock will hit disease programmes that rely heavily on donors.
“All three strategic disease programmes — HIV, TB and malaria — have seen declines in both external and government funding,” the report says. “If this is not addressed soon, the gains made over the years are at risk of being reversed.”
The gaps are stark. HIV programmes face a Sh14.47 billion shortfall against a need of Sh27.11 billion. TB has a Sh13.81 billion gap, while malaria funding falls short by Sh410 million. Across programmes, the commodity funding gap alone stands at Sh34.66 billion.
By contrast, reproductive, maternal, neonatal and child health programmes attracted a larger share of donor money, taking in about a third of all external funding. Support for this area rose to Sh5.85 billion, boosted by a major grant from the Susan Thompson Buffett Foundation.
The Gates Foundation has now emerged as the largest single external contributor overall. Yet even here, government spending has fallen, raising concerns that donor money may be replacing, rather than adding to, public funding.
Loans could help fill some gaps, but analysts caution that borrowing would add pressure to public debt and offer limited short-term returns.
Kenya now faces a difficult balancing act. As a lower middle-income country, access to grants is narrowing just as donor priorities shift. Without fresh financing or a stronger domestic commitment, the country’s fight against its biggest infectious diseases could lose ground.