AbstractThe low‐temperature thermal history of the Holy Cross Mountains (HCM) is investigated by apatite fission track and apatite and zircon (U–Th)/He thermochronology. Our results provide constraints on the deformation history of Palaeozoic basement rocks in the transition area from Precambrian to Palaeozoic Europe that are exposed from beneath Permian–Mesozoic sediments within the HCM. Late to post‐Variscan cooling of the Palaeozoic strata from maximum temperatures is shown to be a major feature of the HCM. This cooling likely followed a heating event related to burial and/or hot fluid circulation along the Holy Cross Fault in the late Carboniferous. The central part of the HCM shows a rapid cooling event caused by tectonic inversion, which started in the Late Cretaceous. However, this event was less pronounced in the western margin of the HCM, where slow cooling continued throughout the Mesozoic with only minor acceleration of the cooling rate since the latest Cretaceous.