ABSTRACT The tectonic evolution of the Karakoram fault in the Pamir Plateau is controversial because the timing and kinematics of several branches of the fault system are unclear. Here we conduct field observations on the East Pamir fault, the North Muskol shear zone, and the Xindi-Waqia fault in the eastern Pamir, and obtain zircon U-Pb and biotite 40Ar/39Ar ages from these ductile shear zones. All three faults/shear zones are hosted by granitic mylonites. The East Pamir fault is a northwest-striking, normal-dextral shear zone that cuts the Rushan-Pshart suture. Zircon U-Pb dating yields a mean age of 201.5 ± 0.5 Ma for the mylonites in this shear zone. Biotite 40Ar/39Ar analysis yields two weighted mean plateau ages, 10.65 ± 0.13 Ma, and 11.04 ± 0.15 Ma. An undeformed granitic vein that cuts the ductile shear zone gives a mean zircon U-Pb age of 9.6 ± 0.3 Ma. We interpret that the granitic protolith crystallized at 201.5 Ma, and the East Pamir fault underwent rapid cooling and exhumation at ca. 11 Ma and ceased by 9.6 Ma. The North Muskol shear zone is an east-striking extensional shear zone along the northern boundary of the Shatput-Muztaghata dome. Two mylonitic samples show mean 206Pb/238U ages of 17.9 ± 0.2 Ma and 17.6 ± 0.3 Ma, which are interpreted as the timing of crystallization of the granitic protolith. The Xindi-Waqia fault is a northwest-striking ductile shear zone and brittle fault that bounds the Muztaghata dome. We obtain two zircon U-Pb ages (231.8 ± 1.1 Ma, 235.9 ± 0.9 Ma) and two biotite 40Ar/39Ar plateau ages (between 6.60 ± 0.10 Ma and 6.87 ± 0.10 Ma) from the mylonites in this fault, and interpret that the granitic rocks were emplaced in the Late Triassic and exhumed in the late Miocene. The newly obtained U-Pb ages, combined with the previously published data, indicate that Rushan-Pshart suture in Pamir marks the closure of an ocean basin within the Palaeo-Tethys Ocean, and cannot be correlated with the Bangong-Nujiang suture in Tibet. We establish a systematic correlation in which the two Palaeo-Tethyan sutures (Tanymas-Jinshajiang and Rushan-Pshart) in Pamir represent the western extensions of the Jinshajiang and Longmu Co-Shuanghu sutures in the Tibetan Plateau, respectively, and the Central Pamir is the western extension of the Tianshuihai-North Qiangtang terrane. This indicates that the dextral slip along the Karakoram fault system in east-central Pamir is 140 ± 10 km, and the mean slip rate since the onset of the Karakoram fault at ca. 18 Ma is 7.8 ± 0.5 mm/yr. Furthermore, our analyses suggest that the North Muskol shear zone was active at ca. 18 Ma before the arrival of the Karakoram fault system then. The East Pamir fault must have been active at ca. 11 Ma, but ceased by ca. 9.6 Ma, and the slip along the Karakoram fault system migrated northeastward and primarily accommodated by the Tashkurgan fault soon after 9.6 Ma. The Xindi-Waqia fault is the southern extension of the ductile shear zone of the Kongur Shan extensional system, as they are highly similar in geometry, kinematics, and timing. Overall, as the Karakoram fault system propagated northward in Pamir during the Cenozoic, crustal deformation migrated northeastward among the Karakoram fault branches from Ladakh to the Kashgar-Yecheng transfer system, and a complex evolution path can be portrayed.