A computational chemistry approach by using a semi-empirical quantum chemical calculation was conducted for fundamental understanding of the adsorption mechanism of the sulfur compounds over the activated carbon adsorbents. The acidic oxygen functional groups, carboxyl and hydroxyl, on the surface were found to be the adsorption sites for selective interaction with the refractory sulfur compounds such as 4,6-dimethyldibenzothiophene. An excellent linear relationship between the estimated heat of adsorption and the experimentally measured selectivity factors was observed. A mechanism for the selective adsorption of the sulfur compounds over the activated carbon was proposed based on a combination of the computational chemistry approach and experimental results. The results imply that the adsorptive performance of the activated carbon for removing sulfur from the liquid hydrocarbon fuels can be improved by increasing the acidic oxygen functional groups on the surface of the activated carbon.