High Ba–Sr granitoids differ from the I-, S- and A-type granitoids, and their petrogenesis and role in the evolution of the continental crust remain enigmatic. This paper reports a study of whole-rock geochemistry, and Sr–Nd isotopes, zircon U–Pb geochronology, and Lu–Hf isotopes of the Zankan high Ba–Sr intrusion in the Central Pamir. U–Pb dating of zircons suggests that the pluton was emplaced during the Miocene (10.2 ± 0.1 Ma). The Zankan rocks have high contents of K2O (3.83 to 12.3 wt%), Rb (212–483 ppm), Ba (701–6910 ppm), and Sr (503–3371 ppm). They have several geochemical characteristics that are consistent with A-type granitoids, such as high Na2O + K2O (8.10–14.2 wt%) and Zr + Nb + Ce + Y (336–1393 ppm) contents. All samples have enriched Sr–Nd–Hf isotope compositions, with 87Sr/86Sri = 0.7097 to 0.7126, εNd(T) = −9.3 to −8.4, and εHf(T) = −12.2 to −4.0. Their isotopic compositions differ from those of mafic lower crust in the Central Pamir. Alternatively, the Zankan rocks may have been derived from an enriched lithospheric mantle. Combining our new isotopic results with data from the literature, we propose that a shift from isotopically juvenile to more isotopically evolved compositions in mantle-derived magmas took place from the Eocene to Miocene. The isotopic shift reveals that South Pamir lower crust was underthrusted beneath the Central Pamir lithosphere during the Miocene. Although high Ba–Sr granitoids generally exhibit “crust-like” isotopic characteristics, our data indicate that they play a role in continental growth.