In 2025, Kenya eliminated a disease it had battled for more than a century and vaccinated more children than ever before. Yet newborns died at the same stubborn rate as before, and the health service was still short of nine in every 10 doctors it needed. 

That is the picture in the World Health Organization (WHO) Kenya Country Office Annual Report for 2025. An independent county-by-county analysis of the report shows a health system moving fast in some directions and standing still in others. 

The pattern has a clear explanation. Campaigns and outbreak response are well funded because major donors prioritise them, while newborn care, primary care and cancer screening compete for a far smaller pool of flexible money. 

The analysis also found at least 12 internal inconsistencies in the report, so several headline figures cannot be cited without caveats. 

A tsetse-borne scourge put to sleep and a vaccination drive for the record books: the year Kenya sprinted 

The biggest achievement of the year made public health history. On June 16, 2025, WHO validated Kenya’s elimination of human African trypanosomiasis (sleeping sickness), as a public health problem. Kenya became the 10th country in the world to reach this milestone, and sleeping sickness is only the second neglected tropical disease it has eliminated, after Guinea worm in 2018. 

Between July 5 and 14, 2025, Kenya ran its largest-ever vaccination campaign. In 10 days, it reached over 16.7 million children with the typhoid conjugate vaccine and 5.4 million with the combined measles-rubella vaccine, achieving national coverage of 87 per cent and 84 per cent respectively. 

Building on that momentum, Kenya became the seventh country worldwide to add the typhoid vaccine to its routine immunisation schedule, given at nine months of age. 

In September 2025, the country ran its first-ever mpox vaccination campaign. Around 90 nurses, vaccinators and surveillance officers delivered 10,697 doses in 10 days across Mombasa, Nakuru and Busia. 

According to the report, the outbreak that began in July 2024 has produced 948 confirmed cases and 13 deaths, a case fatality rate of 1.4 per cent. Of those infected, 807 have recovered, and the rest remain in follow-up. 

From Atlanta to Nairobi, beans in place of tobacco and other quieter gains behind the headlines 

Kenya has also gone almost a year without detecting a single case of polio. A newly upgraded genomic laboratory at the Kenya Medical Research Institute (KEMRI) has cut the time needed to confirm a poliovirus sample from up to 40 days to under 10. 

This work was previously outsourced to a laboratory in Atlanta. The KEMRI laboratory now serves not only Kenya but also Somalia, Ethiopia, Uganda, Djibouti, Eritrea and Yemen. 

Beyond disease control, the Tobacco-Free Farms initiative moved 11,000 to 12,400 farmers away from tobacco and into food crops such as high-iron beans. Women made up half the beneficiaries. 

WHO also handed over $2.3 million (Ksh297.69 million) worth of supplies, including 14 ambulances, oxygen cylinders and 6.5 million tablets for neglected tropical diseases. 

WHO’s programme reached all 47 counties in 2025, and the report names specific activities in 34 of them. Busia, Marsabit, Migori and Siaya each had five distinct named activities, the highest of any county. 

Laboratories in the west, mobile clinics in the north, and the first 28 days of life still the deadliest stretch of all 

The type of support, however, shows a clear geographic divide. Counties in western Kenya such as Bungoma, Kakamega, Vihiga and Trans Nzoia received almost exclusively disease-control, laboratory and digital-systems support, with no outreach or emergency response recorded. 

The arid northern counties, including Marsabit, Samburu, Tana River, Mandera and Garissa, saw the opposite: heavy mobile outreach and emergency response, but little investment in systems or disease control. 

Under-five mortality has fallen dramatically over the long term, from 115 deaths per 1,000 live births in 2003 to 41 in 2022, a 64 per cent decline. 

Newborn mortality, meaning deaths within the first 28 days of life, has not moved. It remains stuck at 21 per 1,000 live births and now accounts for very nearly half of all under-five deaths. That is roughly 30,000 newborns a year, or about four every hour. 

The report says Kenya is not on track to meet Sustainable Development Goal (SDG) 3.2, its child survival target. Most past gains came from immunisation, malaria control and nutrition, which work after the vulnerable newborn period. Newborn survival depends instead on the quality of care during labour and in the first days of life, a workforce and facility problem no vaccination campaign can fix. 

Double the workers but still short-handed, and a first-birthday cliff where vaccine coverage tumbles and measles walks back in 

The workforce problem is severe. Kenya has doubled its health workforce to nearly 190,000 people over the past decade, yet it still meets only 76.4 per cent of estimated need. The shortage of doctors stands at 92 per cent, with just 2.6 doctors per 10,000 people against a WHO-recommended benchmark of 10. 

Nurses fare somewhat better, though the report gives two different pictures. Nurse density, at 22.3 per 10,000, comfortably exceeds the WHO benchmark, yet the same report describes nurses as 46 per cent short of need. 

The gap likely arises because the two figures measure different things. A raw density benchmark counts heads, while a staffing-needs model is calculated from actual facility workloads. Only the second reflects what facilities need to function day to day. 

Immunisation also has a coverage cliff hidden behind its headline figures. Penta3, given at 14 weeks, reaches 89 per cent of children under one. However, the second dose of measles-rubella vaccine, given at 18 months, reaches only around 50 per cent, a gap of roughly 39 percentage points. 

The report links this directly to a resurgence of measles, with 2,118 cases in 2025 and outbreaks persisting since 2021. It notes that Kenya’s last nationwide measles catch-up campaign ran in 2016, nine years earlier. 

High coverage on paper, earmarked money in practice: when the one who pays the piper also calls the tune 

Maternal health shows the same mismatch between coverage on paper and outcomes in practice. Skilled birth attendance and demand for family planning are both reported as high, yet maternal mortality remains at 355 deaths per 100,000 live births. 

Nationally, 15 per cent of girls aged 15 to 19 have already begun childbearing. In Samburu County, the figure reaches roughly 50 per cent, one of the widest disparities recorded anywhere in the report. 

The universal health coverage (UHC) service coverage index has risen from 28 out of 100 in 2000 to 53 in 2025, still short of the 2030 target. Patients still pay 24.2 per cent of total health expenditure out of pocket rather than through insurance or government funding. 

Funding explains much of this. Only around 12 per cent of WHO Kenya’s funding is flexible, assessed core contribution, while the remaining 88 per cent is voluntary and earmarked for specific donor priorities. 

Gavi, the Vaccine Alliance, alone provides 26 per cent, and the United Kingdom contributes 16 per cent through two government departments. Two American private foundations, Myriad and the Susan Thompson Buffett Foundation, together add a further 20 per cent. As a result, immunisation and outbreak response are consistently well resourced, while cancer screening and newborn care compete for a much smaller pool. 

Why campaigns can win a year but only a funded, staffed system can win a generation 

The independent cross-check found at least 12 internal inconsistencies in the report. Cholera deaths in 2025 appear as both six and 13, and the number of health records officers trained appears as 850 in one place and over 1,000 in another. 

Health spending is described both as 7.2 per cent of gross domestic product (GDP) and as 7.2 per cent of the national budget, which are not the same measure. The population at risk of malaria, 57.3 million, exceeds the national population cited elsewhere in the report, 55.3 million. 

None of these discrepancies is serious on its own, and different reporting periods or case definitions may explain some of them. Together, however, they mean several of the report’s headline statistics cannot be cited without caveats. 

In its reflections, WHO Kenya’s leadership says the office sharpened its strategic focus and streamlined its operations during the year. 

The watchpoints it flags for the future are stalled newborn survival, a 92 per cent doctor shortage, underfunded primary care and a widening rural-urban divide. These are exactly the areas where campaigns cannot substitute for a properly staffed and funded everyday health system. 

Text: Yvonne Kawira 
Data analysis and visualisation: Stanley Njihia