A natural brain endocast from the Late Pleistocene site of Ingarano (Apulia, Southern Italy) has been investigated in detail using CT scanning, image processing techniques and Geometric Morphometrics. Our analyses provide relevant information about the taxonomy and taphonomy of the specimen. The external morphology of the endocast was compared to those of the brains of living felids. This combination of techniques is commonly used in palaeoneurology for neuroanatomical and behavioural inferences and enables us to classify the fossil as the first reported natural brain endocast of a Late Pleistocene lynx. In addition, the investigation structure of the internal strctures of the natural endocast aloud us to reconstruct its taphonomic history.