'cephalochordate' originates from New Latin, specifically the word 'Cephalochordata', where Greek 'kephalē' meant 'head' and Greek 'chordē' (or Latinized 'chorda') meant 'string' or 'cord'.

'cephalochordate' changed from New Latin 'Cephalochordata' (a taxonomic name formed in modern biological Latin) and was adopted into scientific English usage in the 19th century as the name for the subphylum; English then also uses the singular form 'cephalochordate' for an individual organism.

Initially it referred primarily to the taxonomic group 'Cephalochordata'; over time it has also been used in English to denote an individual organism of that group or as an attributive adjective (e.g., 'cephalochordate species').