N. cookanum placed within the genus Nautilus, together with extant species based on their shared shell characters. Fossils of the species from the Late Eocene Hoko River Formation are noted as one of the two oldest occurrences for the genus  (with the other, older occurrence being N. praepompilius of the Paleogene).
N. cookanum, a species within the Nautilus genus, is grouped with other living species based on shared shell characteristics and fossils from the Late Eocene Hoko River Formation are among the oldest known occurrences for this genus (along with another older occurrence, N. praepompilius, from the Paleogene).