Ultrasound (US)-assisted synthesis of a N-doped TiO2 catalyst supported on magnetically separable Fe3O4@ZnO particles and its subsequent application for catalytic desulfurization were performed in the present work. The catalyst was also synthesized conventionally to compare the role of acoustic cavitation (US horn working at 20 kHz frequency) in improving the catalyst characteristics. The effects of different ultrasonic (US) power (80 W to 120 W) and duration (15 min to 75 min) were studied to elucidate the best operating conditions for obtaining the minimum particle size of the catalyst. Under optimal conditions of 80 W power and 30 min of time, a minimum particle size of 31.22 μm was obtained. The particle size for the conventionally synthesized catalyst was 806.4 µm, confirming that the particles were agglomerated in the absence of ultrasound. The synthesized catalyst was used for the desulfurization of thiophene to assess the performance of the catalyst, along with a comparative study between the conventionally synthesized catalyst and that obtained using the US-assisted approach. It was evident that the performance of the catalyst synthesized sonochemically was superior, as US enhanced the activity of the catalyst by reducing the particle size and achieving homogeneity. The desulfurization achieved using the sonochemically synthesized catalyst was 47% in 100 min at a 2 g/L catalyst dose and a 3 mL/L H2O2 dose. The desulfurization was only 25% using the conventionally synthesized catalysts under the same operating conditions. Overall, the present work demonstrates the advantages of US in improving the catalyst characteristics, as well as the successful application of catalyst in desulfurization.