The Talas Fergana/Karatau Fault, is a major tectonic boundary separating the Kazakh-Turan domain to the west from the Tian Shan domain to the east. During the Jurassic, movements along the fault led to the opening of several basins. Still, the Mesozoic kinematics of the fault and the geodynamic mechanism that led to the opening of these basins are largely unconstrained. Located at its southwestern termination, the Yarkand-Fergana Basin is certainly the best exposed and however still poorly understood. In this study, we provide new sedimentological description of the Jurassic series from the northern part of the Yarkand-Fergana Basin as well as new palynological data. Following a Middle–Late Triassic period dominated by regional erosion, the onset of sedimentation in the Yarkand-Fergana Basin occurred during the Sinemurian(?)–Pliensbachian. The basin opened as a half graben controlled by the Talas Fergana/Karatau Fault and separated from the Fergana Basin by basement highs. Extension persisted during the late Pliensbachian–Middle Jurassic, leading to a general widening of the Yarkand-Fergana Basin. Finally, Late Jurassic–Early Cretaceous renewed tectonic activity in the area led to the inversion of the north Yarkand-Fergana Basin. The Early to Middle Jurassic timing of development of the Yarkand-Fergana Basin suggests that the coeval movements along the Talas Fergana/Karatau Fault are not associated to the collision of the Qiangtang block along the southern margin of Eurasia. We favor the hypothesis of an opening controlled by transtension related to far field effects of back-arc extension along the Neo-Tethys subduction zone to the west.