The sparse Permian record of actinopterygian fishes remains relatively understudied. As a result, the origins of the morphologically diverse actinopterygian clades of the Triassic, and with them the origins of surviving major lineages, are incompletely understood. One of the few three-dimensionally preserved Permian actinopterygians is Brachydegma caelatum Dunkle 1939, an enigmatic species from the Artinskian (early Permian) of Texas. Brachydegma has had a volatile systematic history, being affiliated with Elonichthys, acrolepids, crown holosteans, and, more recently resolved as a crownward member of the neopterygian stem. This ambiguity in phylogenetic placement stems from limited character information available for Brachydegma, which is restricted to superficial details of the external skeleton. Using computed microtomography (μCT) I investigated the internal anatomy of the two known specimens. Surrounding matrix shows considerable growth of dense (likely iron) minerals that make segmentation difficult, but nevertheless μCT yields considerable new morphological data highlighting an unusual mosaic of characters. Widely distributed actinopterygian traits revealed in Brachydegma include: an aortic canal; a persistent oticooccipital fissure; a perforate hyomandibula; five branchial arches; clavicles capping the anteroventral processes of the cleithra; and a notochord partially constricted by paired neural and haemal elements. Derived features of Brachydegma with a more restricted distribution among actinopterygians include: a parasphenoid stalk that underlies the otic and the anterior part of the occipital regions; well-developed uncinate processes on the epibranchials; and multiple basibranchial ossifications. Distinctive—and potentially autapomorphic— traits include: a broad interorbital septum and a peculiar hyomandibula with a thin dorsal and a much wider ventral limb. These features reinforce recent verbal and cladistic arguments excluding Brachydegma from the neopterygian crown, but the unusual combination of features in this genus and the instability of relationships among ‘early’ actinopterygians precludes a more precise placement at present.