In this work, deep extractive catalytic oxidative desulfurization (ODS) of hydrotreated real diesel fuel was attained using a synthesized catalyst of supported molybdenum oxide on mesoporous silica gel (MoO3/SG) with a high surface area. The characterization of the catalyst was assessed by Fourier transform infrared, X-ray diffraction, Brunauer–Emmett–Teller, Barrett–Joyner–Halenda, N2 adsorption–desorption, scanning electron microscopy, and energy-dispersive X-ray spectroscopy analysis. The effect of molybdenum loading, M catalyst/V oil, H2O2/sulfur molar ratio, temperature, and reaction duration on the ODS of diesel was examined, aiming to set at the optimum values. Different extraction solvents were evaluated, where acetonitrile was processed with the best performance among all. About 99.9% of sulfur in real diesel was selectively removed using the MoO3 (5 wt %)/SG catalyst under the optimal mild reaction conditions of 45 °C, an O/S molar ratio of 8, an M catalyst/V oil of 0.1 g/mL, and a reaction time of 90 min, employing only one step extraction of ODS products by acetonitrile. Compared to previous research studies on ODS of real diesel, an obviously superior performance was exhibited by the introduced catalyst in this study because of the sufficiently large pore diameter, considerably higher surface area (346.5 m2/g) of the catalyst, good distribution of the active phase on the SG surface, and ODS operating at the optimal conditions. Interestingly, no significant loss in catalyst activity was revealed after recycling seven times in ODS of the dibenzothiophene model; however, the catalyst reusability was relatively limited by the interactions of various hydrocarbons in the real diesel. The studies on overall kinetics and reaction pathway were conducted as well.