Despite its declining prevalence, malaria infection remains as the main cause of disease and mortality in Kenya. It is also currently re-emerging in the western highlands due to a combination of climatic and non-climatic factors. The region’s population is highly vulnerable to malaria epidemics and the projected rise in temperature and changes in rainfall patterns may exacerbate existing health risks and create new ones. This report argues that in addition to strengthening the health system and improving collaboration among actors engaged in malaria control and climate risks, two actions should be prioritised for malaria control in the face of climate variability and change: 1) improving the monitoring and prediction of malaria epidemics in all regions by taking into account climate, health and socioeconomic data, as well as by combining local and scientific knowledge; 2) promoting a switch from top-down to more bottom-up targeted interventions adapted to local needs and specificities.