Mesoporous silica of MCM-41 type with spherical morphology was modified with copper, iron, or manganese as well as pairs of these metals by template ion-exchange (TIE) method. The obtained samples were characterized with respect to their structure (XRD), morphology (SEM-EDS), textural parameters (low-temperature N2 sorption), surface acidity (NH3-TPD), transition metal loadings (ICP-OES), their deposited forms (UV-vis DRS) and reducibility (H2-TPR). The catalytic performance of monometallic and bimetallic samples in the selective catalytic reduction of NO with ammonia (NH3-SCR) was tested. The best catalytic results presented a bimetallic copper-manganese sample, which was significantly more active than the mechanical mixture of monometallic copper and manganese catalysts. The synergistic cooperation of manganese and copper species is possibly related to charge relocation between them, resulting in activation of the catalyst in oxidation of NO to NO2, which is necessary for the fast NH3-SCR reaction.