'isoquinoline' originates from Greek and New Latin elements, specifically the Greek word 'isos' meaning 'equal' and the New Latin 'quinoline' (from 'quinic' / 'quinoline' naming in organic chemistry), where 'iso-' meant 'equal' and 'quinoline' referred to the compound related to quinoline.

'isoquinoline' was coined in the late 19th century by chemists as the form 'iso-quinoline' to denote an isomer of 'quinoline'; over time the hyphen was dropped and the standardized modern form 'isoquinoline' came into regular use in chemical nomenclature.

Initially, it meant 'an isomer of quinoline' and this core meaning has remained, though the term is now also used generically for derivatives and substituted isoquinoline compounds.