The production of green fuel oil is of the utmost importance for maintaining a healthy life and environment in the current world. Effective and complete removal of sulfur refractory compounds (such as 4,6-dimethyldibenzothiophene and other alkyl-substituted thiophene derivatives) from fuel oil is essential to meet the new requirements of sulfur standards. Several techniques have been proposed for desulfurization of fuel oil, such as hydrodesulfurization (HDS), selective adsorption, extractive distillation, biodesulfurization, and oxidative desulfurization (ODS). The removal of sulfur by the HDS process requires higher investment costs, high reaction temperature (up to 400 °C), and high pressure (up to 100 atm) reactors. On the other hand, studies have shown that the ODS process is remarkably successful in the removal of sulfur under mild reaction conditions. This review article presents a comparative analysis of various existing catalytic oxidation techniques: acetic acid/formic acid catalytic oxidation, heteropolyacid (HPA) catalytic oxidation, ionic liquid catalytic oxidation, molecular sieve catalytic oxidation, polyoxometalates catalytic oxidation, titanium catalytic oxidation, and ultrasound-assisted oxidation systems, as well as discusses research gaps, and proposes important recommendations for future challenges.