'apoprotein' originates from the Greek prefix 'apo-' meaning 'away from' combined with 'protein' (from Greek 'proteios' meaning 'primary' or 'of first importance').

'protein' comes from Greek 'proteios' (via New Latin/early biochemical Latin) and became established in English as 'protein'; the prefix 'apo-' (Greek ἀπό) was adopted in scientific Neo-Latin/English to indicate separation or absence, and the compound 'apoprotein' arose in 20th-century biochemical terminology to denote the protein lacking its prosthetic group.

Initially assembled from components meaning 'away from' + 'protein', it came to be used specifically in biochemistry to mean 'the protein portion of a conjugated protein lacking its prosthetic group' and has retained that technical sense.