New whole-rock geochemical analyses along with laser ablation multi-collector inductively coupled plasma mass spectrometry U–Pb zircon ages of the granite–rhyolite from the Karakoram Batholith, exposed along the Shyok Valley, NW India, have been performed to understand the timing and geochemical evolution of these magmatic bodies and their implications for the geodynamic evolution of the Karakoram Batholith. New geochronological data on granites and rhyolites along with previously published geochronological data indicate that the Karakoram Batholith evolved during Albian time (~110–100 Ma) owing to the subduction of Tethys oceanic lithosphere along the Shyok Suture Zone. This region witnessed a period of no magmatism during ~99–85 Ma. Following this, the Kohistan–Ladakh arc and Karakoram Batholith evolved as a single entity in Late Cretaceous and early Palaeogene times. Late Cretaceous (~85 Ma) rhyolite intrusions within the Karakoram Batholith show calc-alkaline subduction-related signatures with a highly peraluminous nature (molar A/CNK = 1.42–1.81). These intrusions may have resulted from c. ~13.8 % to ~34.5 % assimilation of pre-existing granites accompanied by fractional crystallization during the ascent of the magma. The contamination of mantle wedge-derived melts with crust of the active continental margin of the Karakoram most likely enhanced the high peraluminous nature of the rhyolite magma, as has been constrained by assimilation fractional crystallization modelling. Two granite samples from the contact of the Shyok Metamorphic Complex and Karakoram Batholith indicate that the post-collisional Miocene magmatism was not only confined along the Karakoram Fault zone but also extends ~30 km beyond the Shyok–Muglib strand.