A new heterogeneous sonocatalytic system consisting of a MoO3/Al2O3 catalyst and H2O2 combined with ultrasonication was studied to improve and accelerate the oxidation of model sulfur compounds of diesel, resulting in a significant enhancement in the process efficiency. The influence of ultrasound on properties, activity and stability of the catalyst was studied in detail by means of GC-FID, PSD, SEM and BET techniques. Above 98% conversion of DBT in model diesel containing 1000 μg/g sulfur was obtained by new ultrasound-assisted desulfurization at H2O2/sulfur molar ratio of 3, temperature of 318 K and catalyst dosage of 30 g/L after 30 min reaction, contrary to the 55% conversion obtained during the silent process. This improvement was considerably affected by operation parameters and catalyst properties. The effects of main process variables were investigated using response surface methodology in silent process compared to ultrasonication. Ultrasound provided a good dispersion of catalyst and oxidant by breakage of hydrogen bonding and deagglomeration of them in the oil phase. Deposition of impurities on the catalyst surface caused a quick deactivation in silent experiments resulting only 5% of DBT oxidation after 6 cycles of silent reaction by recycled catalyst. Above 95% of DBT was oxidized after 6 ultrasound-assisted cycles showing a great improvement in stability by cleaning the surface during ultrasonication. A considerable particle size reduction was also observed after 3 h sonication that could provide more dispersion of catalyst in model fuel.