The new nanocomposite of NaP-Hydroxyapatite (NaP:HAp) has been developed for removal of fluoride from aqueous solution. NaP:HAp nanocomposite has been characterized by using different method such as: X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), Energy Dispersive X-ray analysis (EDAX), surface area (BET) and thermal gravimetric analysis (TGA). Box–Behnken design with three-level and four-factor has been employed for determination of effective process parameters such as solution pH (4–11), temperature (25–55° C), initial adsorbent dose (1–3 g) and initial fluoride concentration (5–25 mg/L) on removal of fluoride from aqueous solution. After 29 batch runs, Quadratic model was established by regression analysis of the experimental data obtained from 29 batch runs. Quantity uptake of fluoride was evaluated using the Langmuir, Freundlich and Dubinin–Radushkevich (DR) models. The rate of adsorption was rapid and followed pseudo-second-order kinetics for this adsorbent. Moreover, thermodynamic parameters (ΔΗ°, ΔG°, ΔS°) for fluoride sorption on NaP:HAp nanocomposite was also studied from the temperature dependence. The significant novelty of this work is the simple preparation of a new nanocomposite from Hydroxyapatite and zeolite that increased stability of HAp in different pH and temperature. Also, this nanocomposite shows high capacity for adsorption of fluoride related of other sorbent and reusable for several times that makes this method nearly green and friendly environmentally.