Abstract The Chulyshman Plateau (CP) is located in the central Siberian Altai Mountains and is bordered by active strike-slip and thrust faults. The current mountainous morphology developed since the Late Miocene to Pliocene by transpressive tectonics as a distant effect of India–Eurasia convergence. The metamorphic basement of the plateau is widely intruded by Palaeozoic granitoids. To constrain the thermo-tectonic history, apatite fission-track (AFT) thermochronology on basement and granitoids was performed. Cretaceous AFT ages ( ∼ 130 – 90 Ma ) were obtained, while mean track lengths ( 13 – 14 μ m ) and length distributions indicate thermal track shortening and prolonged residence in the apatite partial annealing zone. The AFT data were modelled and a three-stage thermal history model was reconstructed. First, a Late Jurassic–Cretaceous cooling is associated with Mesozoic tectonic reactivation of the area. A second stage is a Late Cretaceous–Early Neogene period of stability linked to regional peneplanation. Final cooling is related to denudation of the CP during Late Cenozoic tectonic reactivation.