The abrupt boundary between accreted terranes and cratonic North America is well exposed along the Salmon River suture zone in western Idaho and eastern Oregon. To constrain the post-suturing deformation of this boundary, we assess the cooling history using zircon and apatite (U–Th)/He thermochronology. Pre-Miocene granitic rocks, along a regional transect, were sampled from accreted terranes of the Blue Mountains Province to cratonic North America (Idaho batholith). Each sample was taken from a known structural position relative to a paleotopographic surface represented by the basal unit of the Miocene Columbia River basalts. An isopach map constructed for the Imnaha Basalt, the basal member of the Columbia River Basalt Group (CRBG), confirms the presence of a Miocene paleocanyon parallel to the northern part of Hells Canyon. The (U–Th)/He zircon dates indicate mostly Cretaceous cooling below 200°C, with the ages getting generally younger from west to east. The (U–Th)/He apatite dates indicate Late Cretaceous–Paleogene cooling, which post-dates tectonism associated with the western Idaho shear zone (WISZ). However, (U–Th)/He apatite dates younger than the Imnaha Basalt, with one date of 3.4 ± 0.6 Ma, occur at the bottom of Hells Canyon. These young (U–Th)/He apatite dates occur along the trend of the Miocene paleocanyon, and cannot be attributed to local exhumation related to faults. We propose that burial of Mesozoic basement rocks by the Columbia River basalts occurred regionally. However, the only samples currently exposed at the Earth’s surface that were thermally reset by this burial were at the bottom of the Miocene paleocanyon. If so, exhumation of these samples must have occurred by river incision in the last 4 million years. Thus, the low-temperature thermochronology data record a combination of Late Cretaceous–Paleogene cooling after deformation along the WISZ that structurally overprinted the suture zone and Neogene cooling associated with rapid river incision.