The Jebel Qatrani Formation in the Fayum Depression, Egypt, has yielded a diverse hyracoid fauna that includes both small- and large-bodied forms. Thyrohyrax domorictus is one of the most common hyracoids found in the upper sequence of the Formation, from sites dating to between 29 and 31 Ma. The dental morphology of T. domorictus is more similar to that of living hyraxes than other Paleogene species, but additional morphological evidence is needed to test the hypothesis of procaviid affinities. Two fairly complete crania of T. domorictus are now known and provide a number of additional craniofacial characters for phylogenetic analysis. The specimens are comparable in size to other small-bodied Fayum hyracoids and extant procaviids. T. domorictus has a relatively long rostrum that is perforated by a nasomaxillary fossa, which is also present in Miocene Afrohyrax and Prohyrax and older Thyrohyrax pygmaeus. The anterior border of the orbit is positioned above the molars, and the orbital aperture is closed posteriorly by a complete postorbital bar. Compared to other Fayum hyracoids, T. domorictus exhibits relatively derived, and more procaviid-like, cranial morphology. The cranium of T. domorictus is most similar to that of the extant genus Dendrohyrax, and they share similar morphology of the orbit and cranial roof. Phylogenetic analysis including morphological and molecular data from a large sample of living and extinct afrotherians places Thyrohyrax domorictus as the closest known Paleogene relative of Procaviidae and Pliohyracidae, supporting the hypothesis of procaviid affinities that was originally proposed solely on the basis of dental morphology.