During their long evolutionary history crocodylomorphs achieved a great diversity of body sizes, ecomorphotypes and inferred feeding ecologies. One unique group of crocodylomorphs are the thalattosuchians, which lived during the Jurassic and Cretaceous (ca. 191–125 Ma). They transitioned from shallow marine species, like teleosauroids, into fully pelagic forms with paddle shaped limbs and a vertically orientated tail fluke, the metriorhynchids. The osteological adaptations that allowed metriorhynchids to live in the water are generally well understood, but less is known about their neurosensory and endocranial systems, such as the brain, inner ears, sinuses and cranial nerves and how they relate to their aquatic lifestyle. Based on micro-computed tomography (µCT) data and three-dimensional models, we here describe the braincase and endocranial anatomy of a fully marine metriorhynchid, ‘Metriorhynchus’ cf. ‘M.’ brachyrhynchus (NHMUK PV OR 32617). We found several neuroanatomical features that likely helped this species function in its marine environment. These include a unique flexure in the brain endocast not seen in other thalattosuchians. Other features that have previously been seen in thalattosuchians include enlarged cerebral hemispheres, a hypertrophied venous sinus system, enlarged internal carotid arteries and foramina, and closed/absent lateral pharyngotympanic foramina. The specimen also possesses a pelagic metriorhynchid bony labyrinth morphology, with a compact and dorsoventrally short shape, thick semicircular canals, an enlarged vestibule and potentially a short cochlear duct. A review of character distribution confirms that some of these features evolved at the base of Thalattosuchia in semiaquatic species, long before metriorhynchids became pelagic, suggesting that endocranial anatomy helped allow metriorhynchoids colonize the ocean realm.