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In this work, the potential of a novel hydroxyapatite decorated with carbon nanotube composite (CNT-HAP) for fluoride removal was investigated. The synthesized CNT-HAP composite was systematically characterized by X-ray diffraction(XRD), Fourier Transform infrared spectroscopy(FTIR), scanning electron microscope (SEM) and Brunauer–Emmett–Teller(BET). Batch adsorption experiments were conducted to investigate the defluorination capacity of CNT-HAP. The CNT-HAP composite has a maximum adsorption capacity of 11.05 mg·g−1 for fluoride, and the isothermal adsorption data were fitted by the Freundlich model to calculate the thermodynamic parameters. Thermodynamic analysis implies that the adsorption of fluoride on CNT-HAP is a spontaneous process. Furthermore, the adsorption of fluoride follows pseudo-second-order model. The effects of solution pH, co-existing anions and reaction temperature on defluorination efficiency were examined to optimize the operation conditions for fluoride adsorption. It is found that the optimized pH-value for fluoride removal by CNT-HAP composite is 6. In addition, among five common anions studied in this work, the presence of HCO3- and PO43- could considerably affect the fluoride removal by CNT-HPA in aqueous media. Finally, the underlying mechanism for the fluoride removal by CNT-HAP is analyzed, and an anion exchange process is proposed.