New detrital zircon and isotopic (Nd and Sr) analyses from the eastern Pamir provide information on the depositional age and tectonic terrane affiliation of regional metamorphic terranes. Our results show the following. First, detrital zircon analyses from metasedimentary units along the Kongur Shan extensional system dominantly yield Triassic maximum depositional ages, with a similar age distribution to the Tibetan Songpan‐Ganzi terrane. Further, zircon analyses from quartzofeldspathic gneisses in the core of the Muztaghata massif show the protoliths are Triassic granites. These units are interpreted to be part of the Permian‐Triassic Karakul‐Mazar arc‐accretionary complex terrane. Second, εNd(0) compositions of Triassic granites overlap with other metasedimentary units not analyzed for detrital zircons and are also interpreted to be part of the Karakul‐Mazar terrane. Third, schists in the Sares‐Muztaghata gneiss dome structurally above Triassic orthogneisses yield an Ordovician maximum depositional age with a distinct detrital age distribution similar to the Tibetan Qiangtang terrane and are interpreted to be part of the Central Pamir terrane. Finally, Triassic and Ordovician schists along the Muztaghata massif record an Early Jurassic metamorphic event interpreted to date south‐directed subduction of the Karakul‐Mazar terrane beneath the Central Pamir during final closure of the Paleo‐Tethys. These results, integrated with previously published results and field relations, reveal a complex Mesozoic to Cenozoic interleaving of tectonic terranes in the eastern Pamir with emplacement of the Karakul Mazar terrane both above and below the Kunlun and Central Pamir terranes to the north and south, respectively.