Aluminum containing silica spherical MCM-41 was synthesized and modified with copper by the template ion-exchange method (TIE) and its modified version, including treatment of the samples with ammonia solution directly after template ion-exchange (TIE-NH3). The obtained samples were characterized with respect to their chemical composition (ICP-OES), structure (XRD), texture (low temperature N2 sorption), morphology (SEM-EDS), form and aggregation of deposited copper species (UV-vis DRS), reducibility of copper species (H2-TPR), and surface acidity (NH3-TPD). The deposition of copper by the TIE-NH3 method resulted in much better dispersion of this metal on the MCM-41 surface comparing to copper introduced by TIE method. It was shown that such highly dispersed copper species, mainly monomeric Cu2+ cations, deposited on aluminum containing silica spheres of MCM-41, are significantly more catalytically effective in the NH3-SCR process than analogous catalysts containing aggregated copper oxide species. The catalysts obtained by the TIE-NH3 method effectively operated in much broader temperature and were less active in the side process of direct ammonia oxidation by oxygen.