Zircon and apatite fission track (FT) thermochronology was combined with structural observations and microstructural analyses to assess the history of cooling, deformation, and denudation of the North Patagonian Batholith (NPB) in relation to the movements of the intra-arc Liquiñe-Ofqui Fault Zone (LOFZ) and the northwards migration of the Chile Triple Junction. 56 zircon and 51 apatite FT ages, plus 37 apatite confined track-length distributions were obtained from plutonic and metamorphic rocks in the main Andean Cordillera of southern Chile (41º - 42º15’S). Apatite FT ages and track lengths indicate a stage of rapid cooling at ~5 to 3 Ma along both sides of the LOFZ, whereas older Miocene ages with monotonous cooling histories were obtained further away from the fault. Zircon FT ages range from Cretaceous to Pliocene, with marked differences observed along and across the LOFZ. Three different types of temperature-time histories characterize the post-magmatic cooling of the NPB in the region: deep intrusions with moderate and steady cooling rates, intrusions in the upper crust with very slow cooling rates following a stage of initial rapid cooling, and rapidly cooled and exhumed shallow intrusions, the latter with younger ages towards the fault zone. The most prominent denudation episode along the LOFZ is late Miocene to Pliocene, coeval with plate tectonic reconstructions for the arrival and subduction of the Chile Rise beneath the Taitao Peninsula.