'Pterygotus' originates from Ancient Greek, formed from 'pteryx' (πτερύξ) meaning 'wing' and the suffix '-ōtus' (from ὠτός/ōtós) used in New Latin formation.

'Pterygotus' was coined in taxonomic (New Latin) usage in the 19th century by combining Greek elements; the name has been retained unchanged as the scientific genus name in modern paleontology.

Initially the parts of the name literally referred to 'wing' (and a formative suffix), but over time the compound has come to denote specifically the genus of large, extinct eurypterids rather than a literal 'winged' structure.