The central nervous system of hagfishes displays unique characteristics that are distinct from any other craniate neuroanatomic features. Whether these hagfish characters are general for all craniates, autapomorphies of hagfishes, or merely a derived state of the general cyclostome condition is still a matter of debate that relates to the question of the monophyly or paraphyly of the cyclostomes. The present cladistic study includes 123 neuroanatomical characters of nine chordate species and supports cyclostome paraphyly, in contrast to most current molecular sequence-based phylogenies, which support cyclostome monophyly. An understanding of the unique neural characters in hagfishes is critical to inspiring further comparative and developmental studies with regards to these two conflicting results and the very deep divergence between craniates and their presumed sister groups. The recent access to hagfish developmental data may provide exciting perspectives in the understanding and characterization of the basalmost craniate node and the interpretation of hagfish brain structure.