Adsorption of dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophene (DMDBT) from simulated diesel fuel was investigated with polymer-derived carbon matrices. Sulfur was incorporated to the carbon surface via a high-temperature hydrogen sulfide reduction of oxygen-containing groups. The resultant carbons were characterized by nitrogen adsorption, thermal analysis, potentiometric titration, and elemental analysis. The selectivities for DBT and DMDBT adsorption were calculated with reference to naphthalene. The carbon matrices studied had comparable structures, hence, the effects of the sulfur functionalities were evident in an increase in dibenzothiophenes selectivity and the breakthrough capacity; this was especially visible at a breakthrough point where small pores are expected to be active in the adsorption process. Incorporation of sulfur atoms into the aromatic rings of the carbon matrix increases the ability of the surface to attract dibenzothiophenes via dispersive interactions (sulfur–sulfur bridges). Sulfur and sulfur–oxygen groups present in larger pores enhance the amount of adsorbed dibenzothiophenes via specific acid–base and polar interactions. They also contribute to the reactive adsorption of DBT and DMDBT (oxidized) and their chemisorption on the carbon surface.