We report a geophysical study across an active normal fault in the Southern Apennines. The surveyed area is the “Il Lago” Plain (Pettoranello del Molise), at the foot of Mt. Patalecchia (Molise Apennines, Southern Italy), a small tectonic basin filled by Holocene deposits located at the NW termination of the major Quaternary Bojano basin structure. This basin, on the NE flank of the Matese Massif, was the epicentral area of the very strong 26 July, 1805, Sant’Anna earthquake (I0 = X MCS, Mw = 6.7). The “Il Lago” Plain is bordered by a portion of the right-stepping normal fault system bounding the whole Bojano Quaternary basin (28 km long). The seismic source responsible for the 1805 earthquake is regarded as one of the most hazardous structures of the Apennines; however, the position of its NW boundary of this seismic source is debated. Geological, geomorphological and macroseismic data show that some coseismic surface faulting also occurred in correspondence with the border fault of the “Il Lago” Plain. The study of the “Il Lago” Plain subsurface might help to constrain the NW segment boundary of the 1805 seismogenic source, suggesting that it is possibly a capable fault, source for moderate (Mw < 5.5) to strong earthquakes (Mw ≥ 5.5). Therefore, we constrained the geometry of the fault beneath the plain using low-frequency Ground Penetrating Radar (GPR) data supported by seismic tomography. Seismic tomography yielded preliminary information on the subsurface structures and the dielectric permittivity of the subsoil. A set of GPR parallel profiles allowed a quick and high-resolution characterization of the lateral extension of the fault, and of its geometry at depth. The result of our study demonstrates the optimal potential of combined seismic and deep GPR surveys for investigating the geometry of buried active normal faults. Moreover, our study could be used for identifying suitable sites for paleoseismic analyses, where record of earthquake surface faulting might be preserved in Holocene lacustrine sedimentary deposits. The present case demonstrates the possibility to detect with high accuracy the complexity of a fault-zone within a basin, inferred by GPR data, not only in its shallower part, but also down to about 100 m depth.