The Shyok Suture in western Himalaya preserves a record of the opening and closure of the Mesotethys Ocean between the Shyok ophiolite and Karakoram terrane prior to the India–Eurasia collision. The formation age of the Shyok ophiolite was unknown, which impeded correlation with similar rocks along the Shyok Suture in Pakistan and corresponding sutures in Tibet. We report the first zircon U–Pb ages of a newly documented suite, here named the Changmar Complex. The Changmar Complex gabbronorite and plagiogranite yielded SHRIMP U–Pb zircon Late Jurassic ages of 159.4 ± 0.9 Ma and 151.9 ± 1.5 Ma. Their highly positive initial εHf values (+14.9 to +16.9) indicate a juvenile mantle origin, without continental crust influence on the magma source. The Shyok ophiolite represents either: (1) a separate island arc that preceded formation of the Cretaceous–Eocene Ladakh Arc; or (2) the oldest magmatism and early stage of the Ladakh Arc. Intrusive and extrusive mafic rocks from the Shyok Suture analysed in this study have typical supra-subduction zone enrichment characteristics in their geochemistry and are classified as part of the volcanic-arc ophiolite. The U–Pb age and Hf isotopic signatures for the Shyok ophiolite are similar to the Late Jurassic Matum Das tonalite within the Kohistan Arc; we therefore suggest that they are part of the same intra-oceanic island-arc system that formed in the Mesotethys Ocean prior to Late Jurassic time.