New apatite fission track (AFT) ages have been obtained from a synformal nappe of the Higher Himalayan Crystallines emplaced over the Lesser Himalayan metasedimentary zone of the Arunachal Himalaya, India. The AFT cooling ages within the nappe range between 5.0 ± 0.8 and 14.4 ± 1.3 Ma. Modelled exhumation rates calculated from these cooling ages vary from 0.25 ± 0.12 to 0.69 ± 0.25 mm a⁻¹, which indicates slow exhumation since the Middle to Late Miocene. The AFT cooling ages are younging on both the northern and southern flanks of the synform and the oldest ages are confined to the core. The close mimicking of a shallow crustal exhumation pattern with the synformal structure suggests a strong control of the development of the synform on the exhumation path of the rocks and hence a tectonics–exhumation linkage in the central Arunachal Himalaya. Comparison of these AFT ages with the regional thermochronological record of the Eastern Himalaya reflects a variation in exhumation rates with strike. The AFT age pattern in the central Arunachal Himalaya does not match the pattern of precipitation, which suggests an absence of climate-driven tectonic deformation via focused erosion.