The observed geomorphology and calculated thermal histories of the Bhutan Himalaya provide an excellent platform to test ideas regarding the influence of tectonics and climate on the evolution of a convergent mountain range. However, little consensus has been reached regarding the late Cenozoic history of the Bhutan Himalaya. Some researchers have argued that observed geologic relationships show slowing deformation rates, such that the range is decaying from a geomorphic perspective, while others see the range as growing and steepening. We suggest that a better understanding is possible through the integrated interpretation of geomorphic and thermochronometric data from the comparison of predictions from models of landscape evolution and thermal-kinematic models of orogenic systems. New thermochronometric data throughout Bhutan are most consistent with a significant decrease in erosion rates, from 2–3 km/Ma down to 0.1-0.3 km/Ma, around 6–4 Ma. We interpret this pattern as a decrease in rock uplift rates due to the activation of contractional structures of the Shillong Plateau, an uplifted region ca. 100 km south of Bhutan. However, low-relief, fluvial landscapes throughout the Bhutanese hinterland record a late pulse of surface uplift likely due to a recent increase in rock uplift rates. Constraints from our youngest thermochronometers suggest that this increase in rock uplift and surface uplift occurred within the last 1.75 Ma. These results imply that the dynamics of the Bhutan Himalaya and Shillong Plateau have been linked during the late Cenozoic, with structural elements of both regions active in variable ways and times over that interval.