'Balanoglossida' originates from New Latin, specifically from the genus name 'Balanoglossus' combined with the taxonomic suffix '-ida'; 'Balanoglossus' itself derives from Greek 'balanos' (meaning 'acorn') + 'glōssa' (meaning 'tongue').

'Balanoglossus' was formed from the Greek elements 'balanos' and 'glōssa' to name the genus; later, modern zoological nomenclature applied the suffix '-ida' to create the higher-rank name 'Balanoglossida' for the order of related acorn worms.

Initially the root referred to the genus name meaning 'acorn-tongue'; over time the compound has been used as the name for a broader taxonomic group (the order 'Balanoglossida').