'azathioprine' originates from Modern chemical/International Nonproprietary naming, formed from the prefix 'aza-' (meaning 'nitrogen substitution') plus 'thiopurine' (from 'thio-' meaning 'sulfur' and 'purine', the heterocyclic base).

'azathioprine' was coined in the mid-20th century as a concise name for the compound described chemically (e.g. 'aza-6-mercaptopurine') and became the accepted generic drug name 'azathioprine'.

Initially, the term described the compound's chemical structure ('a nitrogen-substituted thiopurine'), but it has come to be used primarily as the established name for the immunosuppressive drug.