Kenya’s battle against HIV/AIDS which was long sustained by PEPFAR funding is perhaps the hardest hit. With 1.4 million Kenyans dependent on antiretroviral therapy (ART), a projected 32 per cent stockout of HIV medications by November 2025 could reverse decades of progress.
By Aines Wangila, Nairobi
The health of millions of Kenyans now hangs in the balance as the country reels from the devastating effects of a U.S. funding freeze that has stripped the healthcare sector of over Ksh24.9 billion in critical support.
The abrupt suspension of health aid, triggered by a Stop Work Order issued on January 20, 2025, following President Donald Trump’s return to the White House, is rapidly morphing into a full blown public health emergency.
The funding cuts affecting initiatives backed by the President’s Emergency Plan for AIDS Relief (PEPFAR), The United States Agency for International Development (USAID) and the Centers for Disease Control and Prevention (CDC) have exposed Kenya’s heavy reliance on external donors and created a budget gap of Ksh28.4 billion shortfall in a sector that needs at least Ksh80.5 billion to operate effectively.
From HIV/AIDS treatment and malaria control to maternal health and digital health infrastructure, every facet of Kenya’s public health apparatus is feeling the shockwaves. A nation once lauded for its remarkable strides in combating infectious diseases and strengthening health systems now teeters on the edge of a catastrophic collapse.
This is according to a report by Kenya’s Ministry of Health on the impact of the U.S. Government’s Stop Work Order, issued after the enactment of Executive Order No. 14169 by U.S. President Donald Trump in January 2025.
The findings were compiled under the leadership of then Health Cabinet Secretary Dr Deborah Barasa (now Aden Duale), alongside then Medical Services Principal Secretary Harry Kimtai (now Dr Ouma Oluga) and Public Health and Professional Standards Principal Secretary Mary Muthoni Muriuki.
A looming catastrophe for HIV/AIDS treatment
Kenya’s battle against HIV/AIDS which was long sustained by PEPFAR funding is perhaps the hardest hit. With 1.4 million Kenyans dependent on antiretroviral therapy (ART), a projected 32 per cent stockout of HIV medications by November 2025 could reverse decades of progress.
“These medications are not optional, they are life-saving,” said Dr. Emily Nkatha, an infectious diseases specialist at Kenyatta National Hospital. “An interruption not only puts patients at risk but jeopardizes national gains in viral suppression and transmission control.”
Vital services such as viral load testing, adherence counselling, and prevention of mother-to-child transmission (PMTCT) are also at risk. Without these integrated supports, both treatment outcomes and prevention strategies will suffer.
“We’ve invested years in community sensitization and consistent care,” added Dr. Nkatha. “This funding freeze is a betrayal not just of patients, but of public health science.”
Malaria programs disrupted
In malaria-endemic zones like western Kenya, the situation is equally grim. The suspension of Indoor Residual Spraying (IRS) campaigns has exposed vulnerable populations to renewed risk, particularly during the ongoing long rains seasons.
According to the report, the potential layoff of 41,547 health workers supported by U.S. funding is a dire prospect for a system already strained by staff shortages.
“We had finally seen a decline in cases due to consistent spraying and rapid diagnosis,” said James Okello, a community health worker in Siaya County. “Now, test kits will only last eight months and treatment drugs are down to five months. We’re staring at a perfect storm.”
The ripple effect extends to malaria surveillance and monitoring, which are crucial for tracking disease trends and resistance patterns. Without this data, the national response becomes guesswork.
Health workforce on the brink of collapse
According to the report, the potential layoff of 41,547 health workers supported by U.S. funding is a dire prospect for a system already strained by staff shortages.
“These are the doctors, nurses, counselors, lab technicians who are the people who keep the wheels turning,” said Dr. John Mwangi, a senior health administrator in Nairobi. “Telling them their jobs are gone overnight is cruel and short-sighted.”
Loss of experienced professionals would not only cripple service delivery in rural and urban clinics alike but also derail mentorship for younger health workers, weakening the pipeline of future caregivers.
Collapse of digital health infrastructure
Kenya’s investments in electronic medical records (KenyaEMR) and the Kenya Health Information System (KHIS2) have been instrumental in managing chronic diseases and guiding public health decisions. But the halt in funding now threatens their very existence.
Health officials warned that without regular updates, maintenance, and training, the country’s health information systems risk becoming obsolete, which could lead to significant gaps in patient tracking, particularly for HIV and TB delays in responding to emerging health threats, and compromised data-driven decision-making.
“A health system without reliable data is like flying blind,” said Dr. Rachel Nyongesa, a digital health consultant. “We’ll lose the ability to see where the need is greatest.”
Maternal and child health gains at risk
Equally concerning are the disruptions in family planning and maternal health services. Stockouts of contraceptives, now below a five-month threshold, could lead to a spike in unplanned pregnancies, unsafe abortions, and maternal deaths.
“Access to contraception is fundamental to women’s rights and public health,” warned Susan Achieng, a reproductive health advocate. “Denying that access sends us hurtling backward.”
Additionally, antenatal, safe delivery, and postnatal care programs, many of which depend on USAID and CDC funds, face imminent scaling down. The gains made in reducing infant and child mortality are under serious threat.
Government scrambles for stopgap measures
Faced with this unprecedented crisis, the Kenyan government, in collaboration with local and international partners, is scrambling to mitigate the damage and find sustainable solutions. The Ksh8.8 billion allocated by the Treasury to stabilize HIV programs and the Ksh2.7 billion for the National Blood Transfusion Service offer a crucial, albeit temporary, lifeline.
The renewed focus on domestic pharmaceutical manufacturing and the push to accelerate the implementation of Universal Health Coverage (UHC) underscore a growing recognition of the need for greater self-reliance in the health sector.
Engaging the private sector through public-private partnerships is also seen as a vital strategy to bolster supply chains, retain healthcare professionals, and strengthen health infrastructure.
On the diplomatic front, the ongoing bilateral negotiations with U.S. officials are critical. The Kenyan government is urgently seeking a reconsideration of the blanket funding halt, advocating for a phased withdrawal or conditional support to allow for a more managed transition and prevent catastrophic service disruptions.
Experts have warned that the potential destabilization of Kenya’s health system could have serious repercussions across the East African region, given the country’s central role in regional health security through its provision of medical expertise, training, and distribution of essential health commodities.
They cautioned that a weakened Kenyan system might trigger increased cross-border transmission of HIV/AIDS due to disrupted treatment and prevention programs, higher rates of malaria migration as reduced vector control leaves more individuals vulnerable, and disrupted supply chains that could cause shortages in neighboring countries dependent on Kenya.
The unfolding crisis, they added, underscores the interconnected nature of global health and highlights the risks of overreliance on external funding, calling for urgent international dialogue on more sustainable and resilient health financing models for developing nations.
