Agaresuchus fontisensis is an allodaposuchid crocodile from the Campanian–Maastrichtian (Late Cretaceous) of Lo Hueco (Cuenca, Spain). Allodaposuchidae is a clade of European basal eusuchians, which is considered a part of the stem group of Crocodylia. The holotype and paratype skulls of Agaresuchus fontisensis were scanned on computed tomography and their internal cavities, including those of the brain, nerves and blood vessels, as well as the paratympanic sinus system and the paranasal sinuses, digitally reconstructed. The cranial endocast and pneumatic sinuses were then compared with those of other crocodyliforms. The neuroanatomy of Agaresuchus fontisensis resembles those of other mesoeucrocodylians, sharing some morphological traits with extant crocodiles. The neurosensorial and cognitive capabilities inferred from the inner skull cavity reconstructions of Agaresuchus fontisensis are similar to those of other eusuchians. The olfactory acuity of Agaresuchus fontisensis is low by crocodylian standards, closer to that of the alligatoroids rather than to that of the crocodyloids. Its visual acuity is similar to that of Lohuecosuchus megadontos, a sympatric allodaposuchid also found in the fossil site of Lo Hueco.