There have been many studies into the post-Palaeozoic exhumation history of the Irish Sea basin system, which is thought by some to be the locus of Cenozoic exhumation in the British Isles. Few studies, however, have sought to constrain the history of Mesozoic–Cenozoic vertical motions in Northern Ireland, where the geological record of this time period is comparatively complete. Post-Triassic rocks are missing from large parts of the Irish Sea, but sediments of Lower Jurassic, Upper Cretaceous and Oligocene age are found in Northern Ireland, in addition to the Paleocene flood basalts of the Antrim Lava Group. Here we present apatite fission-track analysis (AFTA) and sedimentary rock compaction data from the Larne No. 2 borehole, NE Northern Ireland, which penetrated a c. 2.9 km thick Permian–Triassic succession intruded by Palaeogene dykes and sills. We show that the preserved section was more deeply buried by up to 2.45 km of Upper Triassic–Lower Jurassic sediments that were removed during exhumation episodes beginning during the mid-Jurassic and early Cretaceous. Our results suggest limited early Palaeogene exhumation, which is consistent with the preservation of Upper Cretaceous Chalks beneath the Antrim Lava Group. They also indicate deeper burial of the preserved section by up to 1.3 km prior to late Cenozoic exhumation. This additional section could include a substantial thickness of Paleocene basalt, which provides a likely explanation for the anomalously low porosities of the Chalk in Northern Ireland.