Functionalized SBA-16 mesoporous silica with –SH groups was synthesized using one-pot method. The resulting material was characterized by powder X-ray diffraction, nitrogen gas sorption, FT-Raman spectroscopy. The solid was employed as a Cu(II) adsorbent from aqueous solutions at room temperature. The effects of several variables (stirring time, pH, metal concentration and presence of other ions in the medium) were studied using the batch technique. The results showed that by controlling an optimum molar ratio of 3–4 between tetraethyl orthosilicate (TEOS) and 3-mercaptopropyltriethoxysilane (TMMPS), the synthesized material possessed high order and adsorption capacity for Cu(II) ions though the pore size decreased probably due to the attachment of the organic functional groups in the mesopore channels. The maximum Cu(II) adsorption on this adsorbent occurred in the range of pH 5–6 with an adsorption maximum of 36.38 mg/g. The adsorption of Cu(II) on functionalized SBA-16 mesoporous fitted well to the Redlich–Peterson isotherm equation (r2 = 0.9999) followed by the Langmuir equation (r2 = 0.9847). The involved mechanism might be the adsorption through ligand exchange with the –SH group. The adsorptive competing cations in the aqueous solution had a little effect on the adsorption of Cu(II) on this adsorbent. The presence of different anions (Cl−, , , OAc− and Cit−) influenced the Cu(II) adsorption in the order of . Even after seven regeneration cycles, functionalized SBA-16 mesoporous had a Cu(II) adsorption amount of over 23 mg/g and could be easily regenerated through acid washing, showing a promising application for the treatment of wastewater containing Cu(II) ions.