The movement of magma through the shallow crust and the impact of subsurface sill complexes on the hydrocarbon systems of prospective sedimentary basins has long been an area of interest and debate. Based on 3D seismic reflection and well data, we present a regional analysis of the emplacement and magmatic plumbing system of the Palaeogene Faroe-Shetland Sill Complex (FSSC), which is intruded into the Mesozoic and Cenozoic sequences of the Faroe-Shetland Basin (FSB). Identification of magma flow directions through detailed seismic interpretation of approximately 100 sills indicates that the main magma input zones into the FSB were controlled primarily by the NE–SW basin structure that compartmentalise the FSB into its constituent sub-basins. An analysis of well data shows that potentially up to 88% of sills in the FSSC are <40 m in thickness, and thus below the vertical resolution limit of seismic data at depths at which most sills occur. This resolution limitation suggests that caution needs to be exercised when interpreting magmatic systems from seismic data alone, as a large amount of intrusive material could potentially be missed. The interaction of the FSSC with the petroleum systems of the FSB is not well understood. Given the close association between the FSSC and potential petroleum migration routes into some of the oil/gas fields (e.g. Tormore), the role the intrusions may have played in compartmentalisation of basin fill needs to be taken fully into account to further unlock the future petroleum potential of the FSB.