The cyclostomes, or hagfishes and lampreys, represent the most basal lineage of vertebrates, providing a key to understand craniofacial evolution. While the monophyly of cyclostomes has been supported by recent molecular analyses, phenotypic traits of the hagfish, especially the lack of some vertebrate‐defining features, as well as endodermal origin of the adenohypophysis, have been interpreted as exhibiting more ancestral state than the rest of vertebrates. It is also true that adult craniofacial anatomy of this animal cannot be compared easily with that of the lamprey. To clarify this, the craniofacial developmental pattern of staged embryos of a Japanese inshore hagfish, Eptatretus burgeri, will be described to show that their adenohypophysis arises ectodermally as in other vertebrates, consistent with the molecular phylogenetic data. The above finding also allowed us to identify a pan‐cyclostome embryonic pattern, not shared by crown gnathostomes, and comparative analyses implied that many of the hagfish‐specific traits can be explained by changes secondarily introduced into the hagfish lineage. Since the craniofacial morphology of some basal gnathostomes retains some cyclostome‐like features, we conclude that the pan‐cyclostome pattern would likely reflect the ancestral program for the craniofacial development for the entire living vertebrates.