'archaecraniate' originates from Greek and Greek/Latin word elements, specifically the Greek 'archaios' where 'archae-' meant 'ancient' and the Greek/Latin 'cranium' where 'crani-' meant 'skull'.

'archaecraniate' was formed in modern scientific English by combining the prefix 'archaeo-' (used in names for ancient forms) with 'craniate' (from 'cranium'). The term follows patterns of taxonomic and paleontological coinages in the 19th–20th centuries and has been used in specialist literature to refer to early skull-bearing chordates.

Initially used broadly to denote 'ancient skull-bearing animals'; over time it has come to be used more specifically in paleontological and evolutionary contexts for early members of the craniate stem group.