Deformation on shale-rich continental margins is commonly associated with thin-skinned extension above mobile shales. Normal faulting and shale mobilization are widespread on such margins, being associated with and controlled by progradation and gravitational failure of deltaic sedimentary wedges. However, due to limitations in our ability to seismically imaging these mobile shales, our understanding of how base-shale relief controls deformation, and the shape, size, and distribution of shale structures remain poorly understood. We here use 3D seismic reflection data from the Tarakan Basin, offshore Indonesia to investigate the temporal and spatial evolution of thin-skinned deformations of the Neogene sedimentary section. Our detailed seismic interpretation reveals long (≤ 74 km), concave- and convex-into-the-basin faults, dipping both basinward (eastwards) and locally landward (westwards), which detach downwards on a basal mobile shale (Middle Miocene). The base of the shale unit dips gently (< 17o) seaward, although older (Paleogene), rift-related normal faults mean a local base-shale relief is present. Our analysis of isochron (thickness map) analysis shows that supra-shale normal faulting commenced in the Middle Miocene and was accompanied by the formation of hanging wall rollover folds and associated crestal grabens, with the subsequent along- and across strike migration of strain being related to the nucleation, lateral linkage, and reactivation of individual fault systems. Updip growth faulting was also accompanied by the downslope flow of mobile shale, margin-parallel and-perpendicular differential loading, and local contraction and mobile shale-upbuilding, resulting in the growth of large, margin-parallel shale anticlines further downdip. These faults and anticlines are locally overlain by tall (≤ 5 km) mud diapirs and volcanoes. We suggest that variations in the rate of sediment loading, mobile shale flow, fault growth, and gravitational failure above a seaward-dipping, but slightly rugose base-shale surface, controlled Neogene deformations in the Tarakan Basin. We also demonstrate how variations in the trend and dip of the base-shale surface influences the position, timing, and evolution of supra-shale faults and their associated depocenters along shale-rich, delta-fed clastic margins.