Ongoing climate change poses a major threat to the soil resources of many African countries that mainly rely on an agricultural economy. While arid and semi-arid lands (ASALs) take up most of Kenya’s land mass, approximately 64% of its total croplands lie within mountainous areas with high rainfall, hence, areas highly vulnerable to water erosion. Flooding of the Great Lakes and increasing desertification of the ASALs are illustrative cases of the implications of recent precipitation dynamics in Kenya. This study applied the Revised Universal Soil Loss Equation (RUSLE) to estimate future soil erosion rates at the national level based on four Coupled Model Intercomparison Project v5 (CMIP5) models under two Representative Concentration Pathway (RCP) scenarios. Results showed the current soil loss rate to be at 4.76 t ha−1 yr−1 and projected an increase in average rainfall erosivity under the two scenarios, except for RCP-2.6 (2030s) and (2080s) for the MIROC-5 model. Future projections revealed an incremental change in rainfall erosivity from the baseline climate by a cumulative average of 39.9% and 61.1% for all scenarios by the 2030s and 2080s, respectively, while soil loss is likely to increase concomitantly by 29% and 60%, respectively. The CCCMA_CANESM2 model under the RCP 8.5 (2080s) scenario projected the highest erosion rate of 15 t ha−1 yr−1 over Kenya, which is a maximum increase of above 200%, with the Rift Valley region recording an increase of up to 100% from 7.05 to 14.66 t ha−1 yr−1. As a first countrywide future soil erosion study, this assessment provides a useful reference for preventing water erosion and improving ecosystem service security.