Mesoporous silicas of MCM-41 type modified by transition metal oxides, such as molybdenum, vanadium, and tungsten, were synthesized. These materials were characterized by low-temperature nitrogen adsorption/desorption, Fourier transform infrared spectroscopy, X-ray spectral fluorescence analysis, and transmission electron microscopy techniques and applied for the removal of sulfur compounds in model and real fuels by oxidative desulfurization. The catalysts obtained were tested under optimal conditions. Dibenzothiophene was removed completely, and sulfur removal in gasoline and diesel fractions could reach 91 and 63%, respectively. These catalysts retain their activity in gasoline fraction desulfurization for 5 cycles.