'fluorapatite' originates from modern scientific formation combining 'fluor-' (from Latin 'fluor', used in 'fluorine'/'fluorite') and 'apatite' (from Greek 'apatē'), where 'fluor-' referred to a substance associated with flowing or flux (from Latin root 'fluere' meaning 'to flow') and 'apatē' meant 'deceit' (because the mineral's appearance is variable).

'apatite' came into English via New Latin and French from the Greek word 'apatē' meaning 'deceit'; 'fluor-' was attached in modern mineralogical nomenclature after the element name 'fluorine' (from Latin 'fluor' for fluorspar), producing the compound term 'fluorapatite' to denote the fluoride-bearing variety of apatite.

Initially, 'apatite' (from Greek) referred to the mineral's 'deceptive' appearance; over time the term came to denote a specific group of phosphate minerals. 'Fluorapatite' later came to mean specifically the apatite species containing fluoride (Ca5(PO4)3F).