'apicoectomy' originates from Latin and Greek elements: Latin 'apex, apicis' (via the combining form 'apico-') and Greek 'ektomē', where 'apex' meant 'tip' and 'ektomē' meant 'excision'.

'apicoectomy' was formed in medical New Latin by combining 'apico-' (from Latin 'apex') and '-ectomy' (from Greek 'ektomē'); the variant spelling 'apicectomy' has also been used and both forms influenced modern English usage.

Initially it referred specifically to the excision of a tip or apex; in medical usage it has kept that meaning and now specifically denotes surgical removal of a tooth root tip and related infected tissue.