A new in situ oxidation technology is studied for desulfurization of diesel fuel in a divided-cell trickle bed electrochemical reactor (TBER). In this process, a strong and green oxidizing agent, hydrogen peroxide, is electrogenerated by cathodic oxygen reduction and employed in situ for the oxidation of dibenzothiophene (DBT) in diesel. The cathode in the TBER is made of carbon black and polytetrafluoroethylene particles, giving rise to a highly porous electrode. A maximum concentration of hydrogen peroxide after 2 h electrolysis was obtained at 31.8 mM using potassium hydroxide as electrolyte at constant voltages. A much lower hydrogen peroxide concentration at 18.0 mM was observed under the same conditions but with 10% diesel by volume in the electrolytes. This was attributed to less available electrode areas as well as active sites for oxygen reduction reactions as a result of the presence of the oil diesel phase. Despite this reduction in hydrogen peroxide generation, the DBT in diesel was successfully oxidized in situ in the TBER. A conversion efficiency of 97.8% was achieved in 6 h under liquid circulation operation. The in situ oxidation process is shown to be a novel and feasible technique for deep desulfurization of diesel fuel.