The Mesozoic-Cenozoic basins located between the Faroe, Orkney and Shetland Islands along the NE Atlantic Margin are actively explored oil and gas provinces whose subsidence histories are complicated by multiple tectonic factors, including magmatism, inversion and regional-scale uplift and tilting, that have resulted in spatially variable exhumation. These basins also exhibit nonburial related, transient Cenozoic heating anomalies that make thermal history interpretation and burial history reconstructions problematic. In this study, we have applied a compaction-based approach, which is less susceptible to distortions from transient heating, to provide new constraints on Cenozoic burial and exhumation magnitudes in the UK sector of the Faroe-Shetland region using sonic transit time data from Upper Cretaceous marine shales of the Shetland Group in 37 wells. As estimates of exhumation magnitude depend critically on the form of the normal sonic transit time-depth trend, a new marine shale baseline trend was firstly constructed from shales presently at maximum burial, consistent with other marine shale baseline trends of different ages from nearby basins. Our results indicate that Upper Cretaceous marine shales are presently at or near (i.e. within ≤100 m net exhumation) maximum burial depths in the Møre and Magnus basins in the northeast of the study area as well as in the deeper water Faroe-Shetland Basin (i.e. Flett and Foula sub-basins). However, Upper Cretaceous strata penetrated by wells in the southwest have been more deeply buried, with the difference between maximum burial depth and present-day values (net exhumation) increasing from ca. 200 to 350 m along the central and northeastern parts of the Rona High to ca. 400–1000 m for wells located in the West Shetland Basin, North Rona Basin and southwestern parts of the Rona High. Although the precise timing of exhumation is difficult to constrain due to the complex syn- to post-rift tectonostratigraphic history of vertical movements within the Faroe–Shetland region, our estimates of missing section, together with available thermal history constraints and seismic-stratigraphic evidence, implies that maximum burial and subsequent exhumation most likely occurred during an Oligocene to Mid-Miocene tectonic phase. This was probably in response to major post-breakup tectonic reshaping of this segment of the NE Atlantic Margin linked to a coeval and significant reorganization of the northern North Atlantic spreading system, suggesting that fluctuations in intraplate stress magnitude and orientation governed by the dynamics of plate-boundary forces exert a major control on the spatial and temporal variations in differential movements along complexly structured continental margin.