'gender-atypical' is a compound. 'gender' originates from Old French, specifically the word 'gendre', where the Latin root 'genus' meant 'birth, kind'; 'atypical' originates from Greek via Latin and French, specifically Greek 'a-' meaning 'not' and 'typikos' meaning 'of a type'.

'gender' changed from Old French 'gendre' (from Latin 'genus') and became 'gender' in Middle English; 'atypical' entered English from Greek elements through Latin/French as 'atypicus'/'atypique' and became 'atypical' in modern English. The compound adjective 'gender-atypical' developed in late 20th-century English within medical, psychological, and gender-studies discourse.

Initially, 'gender' referred to grammatical or biological kinds and 'atypical' meant 'not of the usual type'; over time the compound came to mean specifically 'not matching social or cultural expectations for a given gender', as used in contemporary discussions of gender.