'by' originates from Old English, specifically the word 'bi' (also spelled 'by'), where it meant 'near' or 'at'; 'design' originates from Latin, specifically the word 'designare', where 'de-' meant 'from/away' and 'signare' meant 'to mark'.

'designare' passed into Old French as 'desseign'/'design' and into Middle English as 'designe'/'design', while the preposition 'by' comes from Old English 'bi'. The phrase combining the preposition and noun/verb developed in English usage (Middle to Early Modern English) into the modern phrase 'by design'.

Initially related to 'according to a plan or design', the phrase shifted in common use to mean more broadly 'intentionally' or 'deliberately'.