Metallurgical operations, e.g., gold/silver leaching and metal finishing, often produce effluents containing cyanide and cyanide-related compounds such as thiocyanate (SCN-). These industrial effluents can pose an environmental threat due to the toxic characteristics of cyanide species. Thiocyanate is potentially toxic for humans and aquatic organisms due to its low biodegradability and intrinsic toxicity. In humans, thiocyanate ions are neurotoxic, and high blood thiocyanate concentrations may provoke the inhibition of the activity of the various enzyme. In this study, the removal of thiocyanate from aqueous solutions by precipitation in the presence of the hydroxyapatite/graphene oxide nanocomposite was studied. The synthesized nanocomposite was characterized by FT-IR, FESEM, EDS, and XRD analyses. A Box-Behnken design (BBD) was employed for optimization of effective variables on the removal percent of thiocyanate and found as: dosage of the hydroxyapatite/graphene oxide nanocomposite = 0.04 g, initial thiocyanate concentration = 50 mg/L, pH = 5.54, and temperature = 25 °C. The suggested model adequacy was checked by analysis of variance (ANOVA) and other statistical tests. Langmuir, Freundlich, and Dubinin-Raduskovich isotherms were studied. The monolayer adsorption capacity of thiocyanate onto adsorbent is 123.2 mg/g. Adsorption kinetics was studied with the pseudo-first-order, pseudo-second order, and intraparticle diffusion models. The adsorption process followed Langmuir isotherm and pseudo-second order kinetics model. The thermodynamic studies indicate that the thiocyanate adsorption on the adsorbent is an endothermic and spontaneous process. According to the desorption of thiocyanate investigations, acetone was selected as a suitable solvent.