Phylogenetic relationships both within and between the scincomorph families Gerrhosauridae and Cordylidae are in need of re‐examination. Currently the basal gerrhosaurid is unknown, although Angolosaurus skoogi previously was proposed as the sister taxon to mainland African gerrhosaurids. Many details of the cranial osteology of A. skoogi are also unknown because of the rarity in museum collections and elusive lifestyle of this dune‐dwelling lizard, endemic to the Namib Desert. In this study, High‐Resolution X‐ray Computed Tomography (HRXCT) was used to study in detail the cranial osteology of A. skoogi. Results of this study enabled completion of the first anatomical description of the skull and mandible of A. skoogi. Throughout the description, reference is made to a fully labeled cross‐sectional HRXCT data set, available online as supplementary material. Detailed information on cranial osteology obtained from these data can help resolve the contentious placement of A. skoogi within Gerrhosauridae. Unlike other Cordyliformes (Gerrhosauridae + Cordylidae), the post‐frontal in A. skoogi is not extensive and does not extend posteriorly beyond the orbital margin. The squamosal is not bifurcated anteriorly in A. skoogi, unlike other gerrhosaurids. In the braincase of A. skoogi, there is no separate foramen for passage of the glossopharyngeal nerve (cranial nerve IX). This morphological study emphasizes the utility of both HRXCT scans and disarticulated skeletal material as valuable sources of phylogenetically‐informative data. Keywords: Angolosaurus skoogi Cordyliformes, Namib Desert, anatomy, skull, mandible.