Hydroxyapatite (HAp) was successfully synthesized from egg shells, a low cost and easily available biodegradable waste, by the precipitation method and characterized by X-ray diffraction (XRD), scanning electron microscopy, Fourier transform infrared, and Brunauer–Emmett–Teller (BET) surface area analysis. The surface area of HAp was found to be 144 m2/g with a crystalline size of 9–99 nm from the BET and XRD data. The maximum fluoride removal efficiency within 1 h using 0.3 g of the synthesized adsorbent at pH 6 was 95%. The adsorption of fluoride followed second-order kinetics, indicating that chemisorptions are the rate-limiting step. The experimental data were well fitted with Langmuir and Freundlich isotherms, validating both monolayer and multilayer sorption during the fluoride adsorption onto the porous HAp. The positive adsorption of F– ions at the HAp interface can be attributed to ion exchange/ion pairing and H-bonding below the pHpzc of HAp (pHpzc = 8), and the negative adsorption can be attributed to the electrostatic repulsion between O– and F– ions at alkaline pH. Both physical and chemical adsorption phenomena were also evidenced from the molecular parking area data. The results of a batch experiment show that the HAp synthesized from egg shells can be used as an effective, low-cost adsorbent for fluoride removal from a contaminated aqueous solution as well as groundwater compared to other adsorbents.