Nervous systems are important in assessing interphyletic phylogenies because they are conservative and complex. Regarding nervous system evolution within deuterostomes, two contrasting hypotheses are currently discussed. One that argues in favor of a concentrated, structured, central nervous system in the last common ancestor of deuterostomes (LCAD); the other reconstructing a decentralized nerve net as the nervous system of the LCAD. Here, we present a morphological analysis of the nervous system of the pterobranch deuterostome Cephalodiscus gracilis Harmer, 1905 based on transmission electron microscopy, confocal laser scanning microscopy, immunohistochemistry, and computer-assisted 3D reconstructions based on complete serial histological sections. The entire nervous system constitutes a basiepidermal plexus. The prominent dorsal brain at the base of the mesosomal tentacles contains an anterior concentration of serotonergic neurons and a posterior net of neurites. Predominant neurite directions diVer between brain regions and synapses are present, indicating that the brain constitutes a centralized portion of the nervous system. Main structures of the peripheral nervous system are the paired branchial nerves, tentacle nerves, and the ventral stalk nerve. Serotonergic neurites are scattered throughout the epidermis and are present as concentrations along the anterior border of the branchial nerves. Serotonergic neurons line each tentacle and project into the brain. We argue that the presence of a centralized brain in C. gracilis supports the hypothesis that a nerve center was present in the LCAD. Moreover, based on positional and structural similarity, we suggest that the branchial nerves in C. gracilis could be homologous to branchial nerves in craniates, a hypothesis that should be further investigated.