We present the first detailed braincase anatomical description and neuroanatomical study of Portugalosuchus azenhae, from the Cenomanian (Late Cretaceous) of Portugal. This eusuchian crocodylomorph was originally described as a putative Crocodylia and one of the oldest representatives of this clade; however, its phylogenetic position remains controversial. Based on new data obtained from high resolution Computed Tomography images (by micro-CT scan), this study aims to improve the original description of this taxon and also update the scarce neuroanatomical knowledge of Eusuchia and Crocodylia from this time interval, a key period to understand the origin and evolution of these clades. The resulting three-dimensional models from the CT data allowed a detailed description of its well-preserved neurocranium and internal cavities. Therefore, it was possible to reconstruct the cavities of the olfactory region, nasopharyngeal ducts, brain, nerves, carotid arteries, blood vessels, paratympanic sinus system and inner ear, which allowed to estimate some neurosensorial capabilities. By comparison with other crocodylomorphs, these analyses showed that Portugalosuchus, back in the Cenomanian, already displayed an olfactive acuity, sight, hearing and cognitive skills within the range of that observed in other basal eusuchians and crocodylians, including extant species. In addition, and in order to test its disputed phylogenetic position, these new anatomical data, which helped to correct and complete some of the original observations, were included in one of the most recent morphology-based phylogenies. The position of Portugalosuchus differs slightly from the original publication since it is now located as a “thoracosaurid” within Gavialoidea, but still as a crocodylian. Despite all this, to better contrast these results, additional phylogenetic analyses including this new morphological character coding together with DNA data should be performed.