Three 2-D Deep Electrical Resistivity Tomography (ERT) transects, up to 6.36 km long, were obtained across the Paganica-San Demetrio Basin, bounded by the 2009 L'Aquila Mw 6.1 normal-faulting earthquake causative fault (central Italy). The investigations allowed defining for the first time the shallow subsurface basin structure. The resistivity images, and their geological interpretation, show a dissected Mesozoic-Tertiary substratum buried under continental infill of mainly Quaternary age due to the long-term activity of the Paganica-San Demetrio normal faults system (PSDFS), ruling the most recent deformational phase. Our results indicate that the basin bottom deepens up to 600 m moving to the south, with the continental infill largely exceeding the known thickness of the Quaternary sequence. The causes of this increasing thickness can be: (1) the onset of the continental deposition in the southern sector took place before the Quaternary, (2) there was an early stage of the basin development driven by different fault systems that produced a depocentre in the southern sector not related to the present-day basin shape, or (3) the fault system slip rate in the southern sector was faster than in the northern sector. We were able to gain sights into the long-term PSDFS behaviour and evolution, by comparing throw rates at different timescales and discriminating the splays that lead deformation. Some fault splays exhibit large cumulative throws (>300 m) in coincidence with large displacement of the continental deposits sequence (>100 m), thus testifying a general persistence in time of their activity as leading splays of the fault system. We evaluate the long-term (3–2.5 Myr) cumulative and Quaternary throw rates of most of the leading splays to be 0.08–0.17 mm yr−1, indicating a substantial stability of the faults activity. Among them, an individual leading fault splay extends from Paganica to San Demetrio ne’ Vestini as a result of a post-Early Pleistocene linkage of two smaller splays. This 15 km long fault splay can explain the Holocene surface ruptures observed to be larger than those occurred during the 2009 L'Aquila earthquake, such as revealed by palaeoseismological investigations. Finally, the architecture of the basin at depth suggests that the PSDFS can also rupture a longer structure at the surface, allowing earthquakes larger than M 6.5, besides rupturing only small sections, as it occurred in 2009.