This work describes the hydroxyapatite nanoparticle (HAP) preparation from eggshell waste and their application as an adsorbent for Cephalexin (Ceph) antibiotic removal from aqueous solutions. Chemical precipitation with phosphoric acid was used to evaluate the feasibility of calcium oxide for HAP preparation. The structural properties of HAP were characterized by X-ray diffraction, which revealed the formation of the hydroxyapatite crystalline phase formation. In addition, transmitting electron spectroscopy showed an irregular shape with a variation in size. The impact of various experimental conditions on the removal efficiency such as the solution’s pH, contact time, HAP mass, solution temperature, and Ceph concentration were studied. Experimental data showed that HAP could remove most Ceph species from aqueous solutions within 1 h at pH = 7 with 70.70% adsorption efficiency utilizing 50 mg of the HAP. The removal process of Ceph species by HAP was kinetically investigated using various kinetic models, and the results showed the suitability of the pseudo-second-order kinetic model for the adsorption process description. Moreover, the removal process was thermodynamically investigated; the results showed that the removal was spontaneous endothermic and related to the randomness increase. The data confirmed that HAP had high efficiency in removing Ceph antibiotics from an aqueous solution.