'hydroxyapatite' originates from two parts: the chemical prefix 'hydroxy-' (from Greek/Neo-Latin roots 'hydro-' meaning 'water' and 'oxys' meaning 'sharp' or 'acid', ultimately used to denote a hydroxyl group) and 'apatite' (from Greek 'apatēs' meaning 'deceiver'), used in mineralogy to name the apatite group.

'apatite' entered scientific vocabulary via Latin/French from Greek 'apatēs' and was applied to a group of similar phosphate minerals; the compound form 'hydroxyapatite' arose in 19th-century chemical/mineralogical nomenclature to specify the hydroxyl-containing member of that group, and later became common in biological and medical contexts.

Originally 'apatite' referred broadly to a group of visually similar phosphate minerals (name emphasizing that specimens could be 'deceptive'); over time 'hydroxyapatite' came to denote specifically the hydroxyl-bearing calcium phosphate mineral and, in biology, the principal mineral component of bone and enamel.