A new continuous-flow ultrasound assisted oxidative desulfurization (UAOD) process was developed in order to decrease energy and aqueous phase consumption. In this process the aqueous phase is injected below the horn tip leading to enhanced mixing of the phases. Diesel fuel as the oil phase with sulfur content of 1550ppmw and an appropriate mixture of hydrogen peroxide and formic acid as the aqueous phase were used. At the first step, the optimized condition for the sulfur removal has been obtained in the batch mode operation. Hence, the effect of more important oxidation parameters; oxidant-to-sulfur molar ratio, acid-to-sulfur molar ratio and sonication time were investigated. Then the optimized conditions were obtained using Response Surface Methodology (RSM) technique. Afterwards, some experiments corresponding to the best batch condition and also with objective of minimizing the residence time and aqueous phase to fuel volume ratio have been conducted in a newly designed double-compartment reactor with injection of the aqueous phase to evaluate the process in a continuous flow operation. In addition, the effect of nozzle diameter has been examined. Significant improvement on the sulfur removal was observed specially in lower sonication time in the case of dispersion method in comparison with the conventional contact between two phases. Ultimately, the flow pattern induced by ultrasonic device, and also injection of the aqueous phase were analyzed quantitatively and qualitatively by capturing the sequential images.