Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The braincase of Mesosuchus has been previously described, albeit not in detail, and the middle and inner ears were missing. Here, we provide new information based on micro-computed tomography scanning of the best-preserved specimen of Mesosuchus , SAM-PK-6536. Contrary to what has been stated previously, the braincase of Mesosuchus is dorso-ventrally tall. The trigeminal foramen lies in a deep recess on the prootic whose flat ventral rim could indicate the articulation surface to the laterosphenoid, although no such element was found. The middle ear of Mesosuchus shows a small and deeply recessed fenestra ovalis, with the right stapes preserved in situ. It has a rather stout, imperforated and posteriorly directed shaft with a small footplate. These features suggest that the ear of Mesosuchus was well-suited for the detection of low-frequency sounds. The semicircular canals are slender and elongate and the floccular fossa is well-developed. This is indicative of a refined mechanism for gaze stabilization, which is usually related to non-sprawling postures. The most striking feature of the Mesosuchus braincase is, however, the presence of a pneumatic sinus in the basal tubera. The sinus is identified as originating from the pharyngotympanic system, implying ossified Eustachian tubes. Braincase pneumatization has not yet been a recognized feature of stem-archosaurs, but the potential presence of pneumatic foramina in an array of taxa, recognized here as such for the first time, suggests braincase sinuses could be present in many other archosauromorphs.