Apatite fission-track (AFT) data from rocks above and below Lewis thrust fault lying in the footwall and hanging wall of Flathead normal fault record different thermal-history components, depending on individual structural and stratigraphic positions. Apatite fission-track temperature-history models (THMs) indicate that rapid cooling of the Lewis thrust sheet began at about 75 Ma. This cooling coincided with major displacement on the Lewis thrust. Subsequently, folding of the Lewis thrust sheet by underlying thrust duplex culminations formed the Akamina syncline, and a fossil AFT partial annealing zone was superimposed on the syncline. Apatite fission-track data from east of the Flathead graben record a subsequent cooling event during the middle Eocene onward that was coeval with extensional displacement on the Flathead fault and with accompanying uplift and erosion of its footwall. Apatite fission-track data from lower Oligocene sediments in the Flathead graben preserved the temperature history of the sediment source regions in the Lewis thrust sheet without significant subsequent annealing. A set of similar THMs that are consistent with the regional structural history can account for observed variations in AFT parameters at various levels, which are exposed in the Lewis thrust sheet and are penetrated below the thrust sheet by deep wells. From the onset of displacement on the Lewis thrust until the early Oligocene, paleogeothermal gradients in the thrust sheet (8.6–12C/km) were lower than present values (17C/km). The changes in geothermal gradients are attributed to advective heat transfer by tectonically induced, topographically driven, deeply penetrating meteoric water flow. This is a complicated heat-transfer mechanism that can affect organic maturation history and petroleum systems in overthrust belts.