We apply zircon and apatite fission track thermochronology (ZFT and AFT, respectively) to the Variscan crystalline basement of the Mala Fatra Mts (Central Western Carpathians) in order to constrain the thermal history. The samples yielded three Early Cretaceous ZFT ages (143.7±9.6, 143.7±8.3, 135.3±6.9 Ma) and one Eocene age (45.2±2.1 Ma), proving that the basement was affected by a very low-grade Alpine metamorphic overprint. Although the precise timing and mechanisms of the overprint cannot be unequivocally resolved, we propose and discuss three alternative explanations: (i) a Jurassic/Cretaceous thermal event related to elevated heat flow associated with extensional tectonics, (ii) early Late Cretaceous thrusting and/or (iii) an Eocene orogeny. Thermal modelling of the AFT cooling ages (13.8±1.4 to 9.6±0.6 Ma) revealed fast cooling through the apatite partial annealing zone. The cooling is interpreted in terms of exhumation of the basement and creation of topographic relief, as corroborated by the sedimentary record in the surrounding Neogene depressions. Our AFT results significantly refine a general exhumation pattern of basement complexes in the Central Western Carpathians. A younging of AFT ages towards the orogenic front is evident, where all the external massifs located closest to the orogenic front (including Mala Fatra Mts) were exhumed after ~13 Ma from temperatures above ~120 °C.