Indian basement faults, which bound three orogen-perpendicular palaeotopographic ridges of Precambrian Indian basement south of the Himalaya, extend to the base of the Indian lithosphere and to the northern extent of the Indian lithosphere underneath Tibet. In the eastern Himalaya, the active orogen-perpendicular Yadong–Gulu graben is aligned with an earthquake-generating strike-slip fault in the high Himalaya. We argue that the graben results from crustal necking during reactivation of the underplated basement fault. In the central Himalaya, along-strike diachronous deformation and metamorphism within the Himalayan metamorphic core, as well as lateral ramps in the foreland thrust belt, spatially correspond to the Lucknow and Pokhara lineaments that bound the subsurface Faizabad Ridge in the Indian basement. Analogue centrifuge modelling confirms that offset along such deep-seated basement faults can affect the location, orientation and type of structures developed at various stages of orogenesis and suggests that it is mechanically feasible for strain to propagate through a melt-weakened mid-crust. We suggest that inherited Indian basement faults affect the ramp-flat geometry of the basal Main Himalayan Thrust, partition the Himalayan range into distinct zones, localize east–west extension resulting in the Tibetan graben and, ultimately, contribute to lateral variability in tectonic evolution along the orogen's strike.