'antiaggregatory' is formed from the prefix 'anti-' (from Greek anti- meaning 'against') combined with 'aggregate' (from Latin aggregare), plus the adjectival suffix '-ory' (from Latin -orius). 'aggregare' itself comes from Latin elements where 'ad-' meant 'to/toward' and 'gregare' (from grex, gregis) meant 'flock, herd'.

'aggregate' entered English via Latin aggregatus/aggregare and Middle French/Medieval Latin into Middle English as 'aggregate'; the adjective form 'aggregatory' and then the compound with the productive modern prefix 'anti-' produced the specialized medical adjective 'antiaggregatory' in 20th-century medical English.

Initially it literally meant 'against aggregation'; in medical usage it came to be applied specifically to agents or properties that inhibit platelet or cellular aggregation, which is the current specialized sense.