Mesoporous silica was synthesized as a support for the removal of copper ions in aqueous solutions. The Sol-gel method in conjunction with neutral surfactants was used. The remaining surfactants were removed by either the Soxhlet or microwave extraction method. Both extractions resulted in the same pore structure of the mesoporous silicas. However, the microwave extraction method reduced the amount of solvents as well as the time required for removing the remaining organic surfactants. 3-(2-aminoethylamino)propyltrimethoxysilane was functionalized onto the mesoporous silica surface. The functional agent removed copper ions and was bonded to the silica surface via covalent bonding. In addition, it was hydrophilic in nature, which reduced external mass-transfer resistance. The removal capacity of mesoporous silica is about 10 times larger than that of a commercial silica, largely because the mesoporous silica has a larger surface area as well as uniform pore structure. The experimental results and model prediction were in good agreement. The results of sensitivity analysis suggested that the mass transfer rate was so fast that little resistance of external mass transfer and diffusion was possible.