How and when the Pamir formed remains an open question. This study explores Pamir tectonics recorded in a sedimentary section in the eastern Tajik Basin. A prominent lithofacies change that has been recognized regionally is assigned to the middle Miocene (13.5 Ma based on preferred magnetostratigraphic correlation). Closely following this change, detrital zircon U-Pb age spectra and mudstone bulk-rock Nd values exhibit a sediment source change from the Central to the North Pamir estimated ca. 12 Ma. At the same time, the stable oxygen and carbon isotopic values of carbonate cements show negative and positive shifts, respectively. Combined with previous studies in both the Tajik and Tarim basins, these results suggest that the North Pamir experienced a middle–late Miocene phase of deformation and surface uplift. This supports models proposing middle–late Miocene Pamir tectonism, and climate models implying that coeval Pamir orogenesis deflected Westerly moisture and affected Asian environments.