To decipher the thermal history of mineralized systems across the Freegold Mountain area (Yukon, Canada), a combined geochronology (zircon U–Pb and hornblende, biotite, and whole rock Ar–Ar) and thermochronology (apatite and zircon (U–Th)/He) study was carried out. Previous U–Pb data combined with new U–Pb and Ar–Ar data show that intrusive bodies across the Freegold Mountain were emplaced during two protracted episodes, the first spanning from 109.6 to 98 Ma and the second between 79 and 68 Ma. Overprinting of the first intrusive event by a second magmatic hydrothermal event is suggested by a zircon U–Pb age of 108.7 ± 0.4 Ma for a chlorite-altered dyke and a whole rock Ar–Ar plateau age of 76.25 ± 0.53 Ma. Zircon (U–Th)/He data are between 66 and 89 Ma, whereas apatite (U–Th)/He data are scattered (38.7–109.9 Ma) and bracket the two magmatic emplacement events. Our combined data reveal a complex history of reheating that led to resetting of numerous chronometers. In most of the investigated magmatic hydrothermal systems, early fast cooling from igneous emplacement through hydrothermal alteration (between 900 and 200 °C) was followed by later and slower cooling accompanying post mineralization uplift and erosion (between 200 and 70 °C). Preliminary models indicate intrusive bodies associated with the Stoddart Cu–Mo ± W prospect cooled slowly (23 °C/Ma) compared with the ones spatially associated with the Revenue Au–Cu prospect (43 °C/Ma), and the similarity of the zircon U–Pb and (U–Th)/He ages from Revenue dyke further supports a rapid cooling from 700 to 180 °C. Erosion rates of 0.035–0.045 mm/year are consistent with tectonic quiescence during the Late Tertiary combined with the lack of Pleistocene glaciation in central Yukon. Such low rates of exhumation favour the formation and preservation of supergene mineralization, such as that found north of Freegold Mountain.