Knowledge of the tectonic history of the Pamir contributes to our understanding of both the evolution of collisional orogenic belts as well as factors controlling Central Asian aridification. It is, however, not easy to decipher the Mesozoic–Cenozoic tectonics of the Pamir due to extensive Neogene deformation in an orogen that remains largely understudied. This study reports detrital apatite and zircon fission-track (FT) ages from both the eastern Tajik Basin sedimentary rocks and Pamir modern river sands. These FT data, supported by vitrinite reflectance and zircon and apatite U-Pb double dating, suggest that the majority of the FT ages are unreset and record exhumation stages of the Pamir, which has served as the source terrane of the Tajik Basin since the Cretaceous. Further, we combine the new data with a compilation of published detrital apatite and zircon FT data from both the Tajik Basin sedimentary rocks and Pamir modern river sands, to explore the Mesozoic–Cenozoic tectonic history of Pamir. Deconvolved FT Peak Ages document two major Mesozoic exhumation events associated with the Late Triassic–Early Jurassic Cimmerian orogeny that reflects accretion of the Pamir terranes, as well as the Early–early Late Cretaceous deformation associated with the northward subduction of the Neo-Tethys Ocean beneath Pamir. The compiled data also show significant Late Eocene–Neogene exhumation associated with the ongoing formation of the Pamir, which peaks at ~36 Ma, ~25 Ma, ~14 Ma, and ~7 Ma.