Nythosaurus larvatus was one of the first non-mammalian cynodonts to be described, and has played a prominent role in the history of paleoneurology as one of the only representatives of this grade to preserve a natural brain endocast. However, the anatomy and relationships of this taxon are obscure, in large part because the only known specimen is incomplete and partially mouldic. Recent literature has generally treated this taxon as either dubious or synonymous with the best-known Early Triassic cynodont, Thrinaxodon liorhinus. Here, we redescribe N. larvatus based on µCT imaging of the holotype NHMUK PV R1715, revealing the never-before-seen and reasonably well-preserved palate and braincase of this specimen. We demonstrate that Nythosaurus is a distinct taxon, differing from Thrinaxodon in its dental morphology, incomplete secondary palate, and bony labyrinth morphology, in which the posterior semicircular canal is the longest of the three semicircular canals. Inclusion of Nythosaurus in a phylogenetic analysis indicates that it represents a basal epicynodont.