Ionic liquids (ILs), a new class of green solvents, have recently been undergoing intensive research on the removal of thiophenic sulfur species (e.g., dibenzothiophene) from fuels because of the limitation of the traditional hydrodesulfurization method in removing these species. In this work, deep oxidative desulfurization of diesel fuels by six functional acidic ILs are studied, in which ILs are used as both extractant and catalyst, and 30 wt % H2O2 solution as oxidant. These ILs include both Lewis acidic species such as 1-butyl-3-methylimidazolium chloride/2ZnCl2 ([C4mim]Cl/2ZnCl2 and [C4mim]Cl/ZnCl2) and Brønsted acidic species such as 1-methyl-3-ethylcarboxylic acid imidazolium hydrogen sulfate ([CH2COOHmim]HSO4), 1-methyl-3-(butyl-4-sulfinate) imidazolium hydrogen sulfate ([SO3H–C4mim]HSO4), [Hmim]HSO4, and [C4mim]HSO4 where different acidic groups such as −H, −COOH, and −SO3H are appended to the cations. Except for [CH2COOHmim]HSO4, both Brønsted and Lewis acidic ILs are capable of effectively removing dibenzothiophene from model diesel fuels, where 100% sulfur removal is obtained for [C4mim]Cl/2ZnCl2 and [SO3H–C4mim]HSO4. The effects of temperature, molar ratio of O/S, mass ratio of IL/oil, and IL regeneration on desulfurization are investigated systematically for [C4mim]Cl/2ZnCl2 and [SO3H–C4mim]HSO4. The desulfurization ability is not sensitive to the mass ratio of IL/oil, which is desired for reducing IL dosage in industrial application; the ILs can be recycled six times with merely a negligible loss in activity. [C4mim]Cl/2ZnCl2 can reduce the sulfur content in real commercial diesel fuel from 64 to 7.9 ppm with a sulfur removal of 87.7%; however, it is not too effective for coke diesel fuel with high initial sulfur content of 5380 ppm. This work tends to show that diesel fuels can be purified to sulfur-free or ultralow sulfur fuels by further deep oxidative desulfurization by using ILs after hydrodesulfurization.