In Kenya, the heavy rains in April 2024, which triggered flash floods that killed at least 228 people, left 72 others missing and displaced more than 212,000 people, were linked to El Niño 2023. El Niño can trigger extreme events around the globe, causing severe damage to people, animals, and ecosystems. This paper examines the vulnerability of Kenya’s regional health sectors to the 2023 El Niño event and future climate change under different CO2 emission pathways. Using a spatio-temporal analysis of temperature, precipitation, and relative humidity, we show that El Niño led to a significant increase in temperature from May to October 2023 compared to 2022, while extreme precipitation and relative humidity were observed in November. The northeastern region is the most vulnerable to extreme weather events, followed by the eastern region, the coastal region, and the upper parts of the Rift Valley. Future projections show that under SSP3 and higher emission scenarios, the risk of these regions being exposed to extreme heatwaves will increase by more than 60% by 2100. There is an urgent need to address the potential health impacts in vulnerable regions and to prepare and intervene early to prevent future health crises related to ENSO events. We recommend prioritizing these regions in the development of health facilities in Kenya, improving emergency medical care, expanding green spaces, practicing regular hydration, and introducing adequate domestic ventilation to combat health crises from future extreme climate events.