The thermal evolution of distal domains along rifted margins is at present poorly constrained. In this study, we show that a thermal pulse, most likely triggered by lithospheric thinning and asthenospheric rise, is recorded at upper crustal levels and may also influence the diagenetic processes in the overlying sediments, thus representing a critical aspect for the evaluation of hydrocarbon systems. The thermal history of a distal sector of the Alpine Tethys rifted margin preserved in the Ligurian Alps (Case Tuberto-Calizzano unit) is investigated with thermochronological methods and petrologic observations. The studied unit is composed of a polymetamorphic basement and a sedimentary cover, providing a complete section through the prerift, synrift, and postrift system. Zircon fission track analyses on basement rocks samples suggest that temperatures exceeding~240 ± 25°C were reached before~150-160 Ma (Upper Jurassic) at few kilometer depth. Neoformation of green biotite, stable at temperatures of~350 to 450°C, was synkinematic with this event. The tectonic setting of the studied unit suggests that the heating-cooling cycle took place during the formation of the distal rifted margin and terminated during Late Jurassic (150-160 Ma). Major crustal and lithospheric thinning likely promoted high geothermal gradients (~60-90°C/km) and triggered the circulation of hot, deep-seated fluids along brittle faults, causing the observed thermal anomaly. Our results suggest that rifting can generate thermal perturbations at relatively high temperatures (between~240 and 450°C) at less than 3 km depth in the distal domains during major crustal thinning preceding breakup and onset of seafloor spreading.