The assessment of the vulnerability of a site to tsunami events should take into consideration the geomorphological setting, which is strongly determined by the stratigraphic framework of the area. Lampedusa island is located in the central portion of the Sicilian Channel (Mediterranean Sea, Italy), where a significant incidence of tsunamis (with wave runup above 15 m) caused by earthquakes and submarine landslides has been historically documented. This work shows the geomorphological and stratigraphic differences between the western and south-eastern sectors of Lampedusa island. This update to the geological characterization of the island was used to create 3D flooding maps according to runup steps of 5 m, 10 m, and 15 m, thus showing a homogeneous involvement of the south-eastern sector of Lampedusa. Furthermore, our study aims to provide a geomorphological-stratigraphic base for a mathematical-statistical model to create coastal flooding maps due to tsunami waves. As such, this tool is useful for evaluation of strategic infrastructure for the security of the island and the improvement of risk management in civil protection.