The post-Caledonian exhumation history of NW Scotland is a controversial issue, with some studies advocating largely continual emergence whereas others suggest dominantly early Palaeogene plume-driven exhumation. Apatite fission-track analysis (AFTA) data for samples of Precambrian basement and Permian–Cretaceous sediments from onshore and offshore reveal multiple phases of post-Caledonian cooling: Triassic (beginning 245–225 Ma), Cretaceous (140–130 Ma; 110–90 Ma) and Cenozoic (65–60 Ma; 40–25 Ma; 15–10 Ma), all of which are interpreted at least in part as recording exhumation. Basement and sedimentary cover rocks display similar thermal histories, emphasizing the regional nature of these episodes and implying that sedimentary outliers represent the remnants of previously more extensive sequences. Significant thicknesses of Jurassic rocks may once have covered NW Scotland. Palaeocene palaeothermal effects are most pronounced in the vicinity of igneous centres, probably reflecting combined effects of heating by elevated heat flow, deeper burial and hydrothermal activity. Most of the region underwent kilometre-scale Neogene exhumation. Contrary to the common assumption of monotonic cooling and denudation histories, integration of geological evidence with AFTA data defines an episodic thermal history involving repeated cycles of burial and exhumation. We suggest that onshore passive margins and continental interiors may also best be characterized by similar histories.