The Kenya rift valley is the classic example of an active continental rift zone. We report the rift flank cooling history based on a combination of previous apatite fission track (AFT) and new (U-Th)/He (AHe) data. Our results corroborate the Late Cretaceous rapid cooling episode of continent-wide significance revealed previously by AFT dating. Post-Cretaceous cooling of the eastern rift flank was slow with net cooling of <20 °C through much of the Cenozoic. We interpret this cooling style in terms of the absence of significant relief. Samples from the western rift flank and from low elevations of the eastern rift flank reveal a late Neogene cooling episode associated with net cooling of ∼38 °C, indicating that this flank was eroded to a deeper level than that to the east. The late Neogene cooling episode is interpreted as the time of uplift and shaping of the present-day relief of the graben shoulders, which attain elevations of >3400 m in central Kenya. This timing also largely coincides with the uplift of the Western Rift flanks in Uganda and Congo and with the change toward drier conditions and grassland-dominated vegetation in East Africa. We propose that the regional morphotectonic evolution of the Kenyan rift flanks contributed to late Cenozoic environmental change in East Africa, thus superimposing a pronounced local effect on global climate change at that time.