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Abstract The stem lineage of Archosauria is populated by a diverse fossil record that remains notably understudied relative to the crown clade. Prominent among these specimens is a beautifully preserved skull of the early mid-Triassic rhynchosaur Mesosuchus browni [Iziko South African Museum (SAM) 6536], whose phylogenetic position has considerable influence on patterns of pan-archosaurian cranial evolution. We used high-resolution, micro-computed tomography to re-examine the anatomy of this specimen, building on previous studies that were either limited to external observations or restricted to the braincase. A digital segmentation of the cranial elements and primary neurovascular canals of SAM-PK-6536 allows for expanded character scoring and constitutes a foundation for future comparative insights. Our data support the phylogenetically oldest instance of a pneumatized maxilla in a pan-archosaur, bringing the record of antorbital pneumatization into closer alignment with that of the neurocranium. The nasal cavity and primary palate of Mesosuchus includes a complex septomaxilla, a novel element anterior to the vomer, and is likely to have supported a well-developed vomeronasal system. The evolution of this system is discussed in terms of both phylogenetic pattern and how the skeletal architecture of Mesosuchus and other fossils could inform the signalling dynamics that pattern the vomeronasal system during development.