Taphonomic changes can mimic pathological bone lesions and make it difficult to distinguish between ante- and postmortem abnormalities and to perform differential diagnostics. 3D methods, such as CT scanning and 3D printing, can be used as complementary tools to overcome the taphonomic changes. Here, we reconstructed a skull of an interesting archeological case showing severe pathological changes using 3D printing and physical reconstruction. The skeleton belonged to an approximately 18-year-old female. The bones of the entire skeleton exhibited several pathological changes. Both cranium and mandible were asymmetric, with a malformed foramen magnum and left zygomatic process, agenesis of the left external acoustic meatus, cribra orbitalia, and a bilateral absence of mental foramen. The overall diagnostic interpretation was hampered by the extensive taphonomic damage that affected the left side of the skull. In particular, the frontal bone showed taphonomic breakage and plastic deformations were present on the left side of the cranium. The skull was CT-scanned and 3D models of all the single bones were 3D printed and manually re-assembled. The intact reconstructed skull was used to estimate the endocranial volume (ECV). We showed how 3D printing and physical reconstruction of the skull helped overcome the extensive taphonomic alterations; the reconstructed skull provides important diagnostic information such as ECV and a better picture of the original ante-mortem pathological state of the skull.