Carbon aerogels (CAs) were studied as adsorbents for the desulfurization of liquid hydrocarbon fuels for fuel cell applications. A synthetic mixture of dibenzothiophene (DBT) and n-hexadecane (n-HD) was used as a model for sulfur contaminated diesel fuel. Carbon aerogels with two different average pore sizes (4 and 22 nm) were synthesized, characterized, and tested for adsorption of DBT at ambient temperature and atmospheric pressure. The approach-to-equilibrium was monitored, and adsorption isotherms were measured. The CA with the larger average pore size had a higher sulfur adsorption rate and a higher capacity for DBT. The isotherms were best represented by the Freundlich model. According to the Langmuir isotherm, the adsorption capacities of the 4 nm CA and 22 nm CA were 11.2 and 15.1 mg S/g dry CA, respectively. The CAs were found to selectively adsorb DBT over naphthalene, which is a chemically similar but non-sulfur containing organic compound, when both are present in solution. However, the presence of naphthalene slightly reduced the amount of DBT adsorbed.