'antithrombin' is formed from the prefix 'anti-' meaning 'against' and the noun 'thrombin' (a clotting enzyme); 'anti-' ultimately comes from Greek 'anti-' and 'thrombin' derives from New Latin/Greek roots related to clot.

'thrombin' derives from Greek 'thrombos' meaning 'clot' and entered scientific Latin/English as 'thrombin'; the compound 'antithrombin' was coined in modern medical usage (20th century) to denote a substance that counteracts thrombin.

Initially the parts simply denoted 'against thrombin'; over time the compound came to identify a specific plasma inhibitor protein and, later, therapeutic preparations containing that inhibitor.