'balanoglossus' originates from New Latin (scientific Latin), ultimately from Ancient Greek, specifically the words 'balanos' and 'glōssa' (or 'glossa'), where 'balanos' meant 'acorn' and 'glōssa' meant 'tongue'.

'balanoglossus' was formed in New Latin by combining the Greek roots 'balanos' + 'glōssa' to coin a genus name in zoological taxonomy; the compound was adopted into scientific literature as the name for this group of acorn worms.

Initially the components literally signified 'acorn-tongue' (a descriptive compound), but over time the term came to be used specifically as the scientific genus name for certain enteropneust hemichordates (acorn worms).