Long-term climate resilience and poverty eradication in Kenya are expected to be affected by continued global warming. Using observed climate data and projections from a regionally downscaled global climate model, and environmental and socioeconomic data, we mapped hotspots of climate change vulnerability to support the prioritization of resilience-building interventions. Significant decreasing trends in rainfall were found in most of the eastern and coastal areas of the country. High rainfall variability was observed in most arid and semi-arid regions. A higher increase in mean annual temperatures was observed in the cooler highlands of central and western regions and lower in the arid and semi-arid regions. The decreasing trends in rainfall coupled with high variability and increases in mean temperatures were projected to continue. Similarly, hotspots of high vulnerability were mostly located in arid and semi-arid regions. The vulnerability was mainly driven by climate stresses that were observed in these areas including high temperatures, high rainfall variability, decreasing rainfall, and where access to clean water, good housing, health services, and market services was poor. Additionally, these areas had high poverty rates and occupied about 68% of the country with an estimated population of eight million people in 2016. Projections show that “high” vulnerability could increase by 45% and 47% under RCP 4.5 and 8.5 respectively, roping in an additional 5–9 million people by 2050. The vulnerability maps developed here can be used to establish drought impact models that take into account existing adaptation measures, and the expected intensification of vulnerability with climate change. In addition, they can also be used to drive adaptation funding models that are tied to outcomes that result in significant and scalable benefits.