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Abstract The interrelationships of the extant crocodyliansGavialis gangeticusandTomistoma schlegeliihave been historically disputed. Whereas molecular analyses indicate a sister taxon relationship between these two gavialoid species, morphological datasets typically placeGavialisas the outgroup to all other extant crocodylians. Recent morphological‐based phylogenetic analyses have begun to resolve this discrepancy, recoveringGavialisas the closest living relative ofTomistoma; however, several stratigraphically early fossil taxa are recovered as closer toGavialisthanTomistoma, resulting in anomalously early divergence timings. As such, additional morphological data might be required to resolve these remaining discrepancies. ‘Tomistoma’dowsoniis an extinct species of gavialoid from the Miocene of North Africa. Utilising CT scans of a near‐complete, referred skull, we reconstruct the neuroanatomy and neurosensory apparatus of ‘Tomistoma’dowsoni. Based on qualitative and quantitative morphometric comparisons with other crocodyliforms, the neuroanatomy of ‘Tomistoma’dowsoniis characterised by an intermediate morphology between the two extant gavialoids, more closely resemblingGavialis. This mirrors the results of recent studies based on the external anatomy of these three species and other fossil gavialoids. Several neuroanatomical features of these species appear to reflect ecological and/or phylogenetic signals. For example, the ‘simple’ morphology of their neurosensory apparatus is broadly similar to that of other long and narrow‐snouted (longirostrine), aquatic crocodyliforms. A dorsoventrally short, anteroposteriorly long endosseous labyrinth is also associated with longirostry. These features indicate that snout and skull morphology, which are themselves partly constrained by ecology, exert an influence on neuroanatomical morphology, as has also been recognised in birds and turtles. Conversely, the presence of a pterygoid bulla inGavialisand several extinct gavialoids, and its absence inTomistoma schlegelii, could be interpreted as a phylogenetic signal of crocodylians more closely related toGavialis than toTomistoma. Evaluation of additional fossil gavialoids will be needed to further test whether these and other neuroanatomical features primarily reflect a phylogenetic or ecological signal. By incorporating such previously inaccessible information of extinct and extant gavialoids into phylogenetic and macroecological studies, we can potentially further constrain the clade's interrelationships, as well as evaluate the timing and ecological association of the evolution of these neuroanatomical features. Finally, our study supports recent phylogenetic analyses that place ‘Tomistoma’dowsonias being phylogenetically closer toGavialis gangeticusthan toTomistoma schlegelii, indicating the necessity of a taxonomic revision of this fossil species.