Temnospondyls form a large clade of extinct non-amniotic tetrapods. Although their external cranial anatomy is relatively well known, their endocranium (i.e. internal structures of the skull) remains poorly known due to the lack of well-preserved material with conservation of the original anatomic volume. Internal structures are generally crushed under the skull roof due to the frequent flattening of skulls during fossilization. Yet this region is of great paleobiological interest with respect to the hearing, nervous, and vascular systems. In addition, endocranial characters have already been shown to be phylogenetically very informative in various vertebrate groups (e.g. mammals, dinosaurs). An exquisite skull belonging to Stanocephalosaurus amenasensis from the Lower-Middle Triassic of the Zarzaïtine Series (Algeria) has been investigated by X-ray micro-CT (computed tomography) scan. The resulting 3-D reconstruction of this unique specimen reveals highly detailed anatomy of the endocranial region, which is described herein. In addition, both columellar cavity and stapes morphologies lead to a new functional hypothesis for the stapes as part of an underwater hearing system. This endocranium description increases our knowledge of temnospondyl paleobiology and endocranial structure variability. The hearing system postulated in S. amenasensis provides an evolutionary scenario which is also compared with that of extant anurans.