A well-preserved braincase of the basal alligatoroid Diplocynodon tormis was found in the middle Eocene site of ‘Teso de la Flecha,’ Salamanca, Spain. The specimen was scanned using computed tomography (CT), and its inner cavities were digitally rendered in three dimensions. Most bones of the left side are missing, so the reconstruction was based mainly on the right half of the braincase. The endocast of the brain cavity, nerves, part of the inner ear, and blood vessel canals was reconstructed, as well as a complex network of air-filled cavities around the hindbrain formed by the median pharyngeal sinus and pharyngotympanic sinus systems. Inner cavities of the skull are considered to be conservative structures. The comparison of this specimen with several extant crocodilians (Alligatoroidea, Crocodyloidea, and Gavialoidea) allows us to identify a neuroanatomical evolutionary pattern that matches current phylogenetic hypotheses. All internal cavities of the braincase of Diplocynodon are similar to those of other studied eusuchians, with some noteworthy differences in shape and size, particularly regarding the cerebrum and the paratympanic sinus system. Diplocynodon tormis shows a combination of alligatoroid synapomorphies and crocodylian symplesiomorphies in its internal cavities, consistent with its phylogenetic placement as a basal alligatoroid.