Thiophenic compounds are considered one of the major obstacles in deep desulphurization of transportation gasoil. In this paper, a single-stage reactor, in which the induction of hydrogen peroxide, oxidation of thiophenes, and adsorption of sulphones from model fuel was demonstrated in one single step at mild temperatures. In our proposed mechanism, the removal of thiophenes from model fuel undergoes three stages: 2-propanol dehydrogenation and in situ generation of hydrogen peroxide, oxidative desulphurization, and the adsorption of sulphones on active carbon. Palladium/active carbon (Pd/C) was not only used to catalyze the production of hydrogen peroxide, but also guarantees efficiency in the adsorption of sulphones from the oil phase and aqueous phase owing to its large specific surface area and pore volume. Thus, the goal to get ultra-low sulphur fuel was well achieved under optimal conditions after almost all the sulphones had entered into the pores of active carbon and stayed in the adsorbent. Accumulation of sulphur in active carbon inhibits further desulphurization operation. Washing with excessive anhydrous ethanol, the efficiency of Pd/C was almost fully recovered.