Detailed descriptions of braincase anatomy in early diapsid reptiles have been historically rare given the difficulty of accessing this deep portion of the skull, because of poor preservation of the fossils or the inability to remove the surrounding skull roof. Previous descriptions of the braincase of Youngina capensis, a derived stem-diapsid reptile from the Late Permian (250 MYA) of South Africa, have relied on only partially preserved fossils. High resolution X-ray computed tomography (HRXCT) scanning, a new advance in biomedical sciences, has allowed us to examine the reasonably complete braincase of the holotype specimen of Youngina capensis for the first time by digitally peering through the sandstone matrix that filled the skull postmortem. We present the first detailed 3D visualizations of the braincase and the vestibular system in a Permian diapsid reptile. This new anatomical description is of great comparative and phylogenetic relevance to the study of the structure, function and evolution of the reptilian head.