Sediments infilling in intermontane basins in areas with high seismic activity can strongly affect ground-shaking phenomena at the surface. Estimates of thickness and density distribution within these basin infills are crucial for ground motion amplification analysis, especially where demographic growth in human settlements has implied increasing seismic risk. We employed a 3D gravity modeling technique (ITerative RESCaling—ITRESC) to investigate the Fucino Basin (Apennines, central Italy), a half-graben basin in which intense seismic activity has recently occurred. For the first time in this region, a 3D model of the Meso-Cenozoic carbonate basement morphology was retrieved through the inversion of gravity data. Taking advantage of the ITRESC technique, (1) we were able to (1) perform an integration of geophysical and geological data constraints and (2) determine a density contrast function through a data-driven process. Thus, we avoided assuming a priori information. Finally, we provided a model that honored the gravity anomalies field by integrating many different kinds of depth constraints. Our results confirmed evidence from previous studies concerning the overall shape of the basin; however, we also highlighted several local discrepancies, such as: (a) the position of several fault lines, (b) the position of the main depocenter, and (c) the isopach map. We also pointed out the existence of a new, unknown fault, and of new features concerning known faults. All of these elements provided useful contributions to the study of the tectono-sedimentary evolution of the basin, as well as key information for assessing the local site-response effects, in terms of seismic hazards.