The application of Ground Penetrating Radar (GPR) prospecting to the search of fossil structures, particularly using advanced techniques like Finite-difference time-domain (FDTD) modelling and GPR attribute analysis, is currently poorly exploited in paleontology. Here, we promote the use of such a GPR workflow at Bargiano (Umbria, central Italy), a unique paleontological site known for the discovery of cetacean skeletons, dolomitized sperm-whale cololites (Ambergrisichnu salleronae), and layered fossil assemblages. The study site is characterized by a very uneven topography shaping highly conductive clayey deposits, representing not exactly ideal conditions for GPR surveying. After generating models encompassing a real topography and variable electrical properties of media, we simulated buried fossil structures at variable depth with different size and geometry, using different operative frequencies. After obtaining information on the characteristics of reflections, investigation depth, and detectability, we provide a comparison with experimental data, also used to compute instantaneous amplitude and phase attributes. Upon depicting a peculiar GPR signature for our targets, we discuss the results in light of ground-truthing performed through trenching. Our workflow allowed us to restrict the excavation areas, extending the surface information in depth in a non-invasive way, and optimizing the field operations, necessary for the preservation of the study site.