The transition from water to land by the earliest tetrapods in the Devonian Period is seen as one of the greatest steps in evolution. However, little is understood concerning changes in brain morphology over this transition. Here, we determine the brain–braincase relationship in fishes and basal lissamphibians as a proxy to elucidate the changes that occurred over the fish–tetrapod transition. We investigate six basal extant sarcopterygians spanning coelacanths to salamanders (Latimeria chalumnae, Neoceratodus, Protopterus aethiopicus, P. dolloi, Cynops, Ambystoma mexicanum) using micro-CT and MRI and quantify the brain–braincase relationship in these extant taxa. Our results show that regions of lowest brain–endocast disparity are associated with regions of bony reinforcement directly adjacent to masticatory musculature for the mandible except in Neoceratodus and Latimeria. In Latimeria this deviation from the trend can be accounted for by the possession of an intracranial joint and basicranial muscles, whereas in Neoceratodus difference is attributed to dermal bones contributing to the overall neurocranial reinforcement. Besides Neoceratodus and Latimeria, regions of low brain–endocast disparity occur where there is less reinforcement away from high mandibular muscle mass, where the trigeminal nerve complex exits the braincase and where endolymphatic sacs occupy space between the brain and braincase wall. Despite basal tetrapods possessing reduced adductor muscle mass and a different biting mechanism to piscine sarcopterygians, regions of the neurocranium lacking osteological reinforcement in the basal tetrapods Lethiscus and Brachydectes broadly correspond to regions of high brain–endocast disparity seen in extant taxa.