Abstract There is a growing consensus that pterosaurs and the flightless Lagerpetidae are closely related. This relationship is supported by apomorphies throughout the skeleton, including endocranial character states such as a well‐developed floccular fossa and a tall anterior semicircular canal. Our knowledge of lagerpetid anatomy has been improved by recent discoveries. Among them, the Brazilian record plays a significant role, having produced two described species, Ixalerpeton polesinensis and Venetoraptor gassenae , and several more fragmentary specimens. In this study, we used an x‐ray micro‐computed tomographic scan to describe the endocranial anatomy of the holotype of Venetoraptor gassenae . The endocranial anatomy of Venetoraptor gassenae is similar in shape to that of other described lagerpetids, and we reach the following conclusions: (1) in pterosaurs, the metotic foramen exits posteriorly, whereas in lagerpetids and dinosauromorphs it exits through the lateral wall of the braincase; and (2) Venetoraptor gassenae is unique among lagerpetids in having only one exit for cranial nerve XII, expanding its differential diagnosis. These differences highlight that the braincase anatomy of lagerpetids is aligned with the anatomical disparity observed in the group. Finally, we discuss why future studies should focus on comprehending patterns of braincase pneumaticity in avemetatarsalians.