The Albanerpetontidae, small salamander-like tetrapods from the Middle Jurassic-Neogene of Laurasia and northern Africa, are widely considered to be lissamphibians; however, relationships among major lissamphibian clades are unresolved. A recently identified, isolated, and three-dimensionally preserved neurocranium (early Pliocene, Hungary) referred to Albanerpeton pannonicum is described, incorporating information gained from the application of micro-computed tomography. It is revealed that the neurocranium is a robust, box-like structure composed of the coossification of the parasphenoid, otic capsules, and occipital elements. The otic capsule endocast reveals the morphology of the endosseous labyrinth, complete with well-defined endosseous semicircular canals and a modestly developed ventral endosseous auditory region; however, details of the individual auditory organs are not discernable from the endocast. Features of the neurocranium and endosseous labyrinth are consistent with the hypothesis that A. pannonicum, and albanerpetontids in general, were somewhat fossorial. The neurocranium and endosseous labyrinth exhibit a mosaic of anuran, urodele, and apodan traits, thus precluding refinement of the phylogenetic position of albanerpetontids. In general, the neurocranium and endosseous labyrinth appear most similar to urodeles, and similarities with apodans and anurans may be due to convergent evolution resulting from similar habits and responses to inner ear stimulation. This new neurocranium represents the best-known specimen of its kind for albanerpetontids, and the data presented here combined with future comparative studies will contribute to a better understanding of the biology and evolution of this group.