The crisis stems from a precipitous drop in external health funding, which plummeted by 71.69 billion shillings from 126.09 billion shillings in the 2024-25 fiscal year to 54.40 billion shillings in 2025-26, according to an analysis by the University of Nairobi’s Centre for Epidemiological Modelling and Analysis.
“For commodities, the funding gap across HIV, TB, malaria, vaccines and nutrition is estimated at Sh34.7 billion in the financial year 2025/26, excluding the overfunded Reproductive, Maternal, Newborn and Child Health programme,” the center said in its assessment report.
The maternal and child health program, jointly administered by Kenya’s Health Ministry, the World Health Organization, UNICEF, UNAIDS, UNFPA and UN Women, focuses on reducing mortality rates in underserved regions and has not experienced the same funding constraints.
The projected shortfall threatens to destabilize a medical supply system that has relied heavily on American taxpayer dollars for two decades, particularly for antiretroviral drugs, tuberculosis medicines and disease prevention programs.
Two-decade dependency unravels
Since the early 2000s, the United States government — primarily through the President’s Emergency Plan for AIDS Relief — has underwritten the majority of Kenya’s HIV medications, tuberculosis treatments and communicable disease control initiatives.
This assistance arrived through two distinct channels. A portion passed through Kenya’s Treasury as official development assistance and appeared in government budgets, while the majority flowed directly to health programs outside the formal budget process, creating a parallel health delivery system alongside government facilities.
Off-budget funding has now contracted from 87.37 billion shillings in 2024-25 to 26.46 billion shillings in 2025-26, representing a decline of nearly 70 percent. These funds previously covered essential medicines, laboratory equipment, health worker salaries and pharmaceutical distribution to rural clinics throughout the country.
On-budget external funding also decreased, falling from 39 billion shillings to 28 billion shillings over the same period. The most significant reductions came from the Global Fund to Fight AIDS, Tuberculosis and Malaria, which cut 11.6 billion shillings, and the World Bank, which reduced its commitment by 1 billion shillings.
David Khaoya, lead researcher at the epidemiological center, said external funding has long played an outsize role in Kenya’s health sector but remains inherently unpredictable and unsustainable.
“This funding shock is a wake-up call,” Khaoya said. “Kenya and other African countries now have an opportunity to rethink how health systems are financed and build long-term resilience.”
Vulnerable populations face treatment disruption
The timing of the funding contraction carries particular urgency. Approximately 1.4 million Kenyans live with HIV, representing an adult prevalence rate of 4.9 percent, according to health ministry data.
The country also records approximately 140,000 new tuberculosis cases annually, with the disease claiming roughly 23,000 lives each year. Malaria remains endemic, with an estimated 3.5 million cases reported annually and about 70 percent of the population residing in areas at risk of transmission.
The analysis identifies five categories facing the largest funding gaps, each carrying serious public health implications.
HIV medications face the biggest shortfall, estimated at 14.47 billion shillings. These antiretroviral medicines are taken daily by more than 1.2 million Kenyans to suppress viral load and maintain normal, productive lives.
Without adequate supplies, treatment interruptions could occur, increasing the risk of drug resistance and onward transmission of the virus to uninfected individuals.
Winnie Byanyima, executive director of the Joint United Nations Programme on HIV/AIDS, warned that the funding crisis threatens hard-won epidemiological gains.
“Behind every data point in this report are people — babies and children missed for HIV screening or early diagnosis, young women cut off from prevention support, and communities suddenly left without services and care,” she said.
Closely linked to the HIV crisis is a 13.81 billion shilling shortfall in tuberculosis medicines. TB and HIV frequently occur together, with people living with HIV up to 18 times more likely to develop active tuberculosis.
TB treatment requires strict adherence to daily medication regimens for six to nine months. Interruptions can lead to drug-resistant tuberculosis, a more dangerous and costly form of the disease that requires extended treatment with second-line medications.
The report warns that supply disruptions could reverse years of epidemiological progress and potentially increase the estimated 23,000 TB deaths recorded annually.
Immunization programs at risk
Childhood vaccines face a 3.09 billion shilling funding gap, threatening Kenya’s relatively strong immunization coverage rates.
The shortfall affects vaccines protecting against pneumonia, diarrheal diseases, polio, measles and other deadly childhood illnesses. Approximately 86 percent of Kenyan children currently receive basic immunizations.
However, reduced funding could delay routine immunizations, raising the risk of outbreaks in areas where coverage falls below herd immunity thresholds required to prevent disease transmission.
Malaria programs face a 410 million shilling funding gap. Funding for malaria control fell sharply after the Global Fund allocated 1.53 billion shillings for 2025-26, down from 4.25 billion shillings the previous year.
The disease still causes an estimated 3.5 million cases and approximately 10,700 deaths annually, most among children under five years of age.
The funding cuts mean fewer insecticide-treated mosquito nets, reduced indoor residual spraying campaigns and lower stocks of antimalarial medicines and rapid diagnostic test kits. Unlike HIV, malaria case numbers can rebound quickly when vector control efforts weaken.
“Budgets for all three strategic disease programmes have declined due to reduced external funding and lower domestic allocations, raising serious risks of reversal in hard-won gains in incidence, treatment coverage and mortality,” the report stated.
Kenya’s health sector receives funding primarily from the government, which provides 53 percent, followed by the private sector at 23 percent and external funders at 18 percent, according to the 2018-19 national health accounts, the most recent comprehensive assessment available.
In that fiscal year, the United States contributed more than 60 percent of all external health funding. Strategic disease programs such as HIV, tuberculosis and malaria remain heavily dependent on donor support.
External funders financed 62 percent of HIV health expenditure in 2018-19 and paid for 86 percent of antiretroviral medications, with half coming from the U.S. government.
Although Kenya allocated 138.1 billion shillings to health in the 2025-26 budget — an 8.7 percent increase from the previous year — this remains below the Abuja Declaration target of 15 percent of total government spending on health.
African Union member states committed to this threshold in 2001 to strengthen health systems across the continent, but few countries have consistently met the goal.
“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 concluded.
The funding crisis extends beyond Kenya. Several East African nations that relied on similar donor support structures face comparable challenges as international development assistance priorities shift and domestic resource mobilization remains constrained.
Health policy experts suggest the crisis may accelerate regional discussions about sustainable health financing mechanisms, including increased domestic revenue allocation, regional pharmaceutical procurement cooperation and innovative financing instruments such as health insurance schemes and sin taxes on tobacco and alcohol.
However, immediate solutions remain elusive as Kenya’s government grapples with competing fiscal pressures, including debt service obligations, infrastructure development and education spending.
The pharmaceutical supply chain disruption comes as Kenya’s healthcare workers continue to demand better working conditions and improved remuneration, adding further strain to an already stressed system.
Without rapid intervention — either through restored donor funding, dramatically increased domestic health spending or emergency pharmaceutical procurement mechanisms — hospitals across Kenya may begin experiencing stock-outs of critical medications within months, health officials warn.
The crisis underscores the vulnerability of health systems heavily dependent on external financing and the challenges facing nations transitioning toward self-reliance in essential health services.
International health organizations have expressed concern about the broader implications for global health security. Disease control experts note that treatment interruptions in high-prevalence settings could facilitate the emergence of drug-resistant pathogens, potentially complicating treatment protocols worldwide.
Kenya’s experience serves as a cautionary tale for other middle-income countries graduating from traditional development assistance programs. As nations reach higher income classifications, they often lose eligibility for concessional financing before domestic revenue systems can adequately support essential services.
The transition period presents particular challenges for health systems, where infrastructure investments and skilled personnel requirements demand sustained, predictable funding streams that may take years or decades to establish through domestic taxation alone.
