Three-dimensional graphenic adsorbents have been successfully synthesized by hydrothermal reduction and applied for deep removal of dibenzothiophene (DBT) from model fuel. The nanoporous spongelike structure of the graphenic compounds was confirmed using various characterization techniques. Reduced graphene oxide (rGO), carbon black graphene composite (CB-G), and nickel impregnated graphene (Ni-G) showed adsorption capacities of 41.8, 46.9, and 43.3 mg of DBT g(-1), respectively, and the DBT concentration in the model fuel was diminished to less than 10 ppm. Thermodynamic parameters for the adsorption process evidenced feasible and exothermic adsorption on rGO and CB-G with negative enthalpy changes. Adsorption isotherms for rGO and CB-G were best fitted with the Langmuir isotherm, indicating uniform adsorption sites. On the other hand, the isotherms for Ni-G were best fitted with the Freundlich and Temkin models, showing special active sites. Carbon black intercalation can effectively change the pore dimensions to meso size while maintaining a uniform graphenic morphology, leading to high DBT adsorption capacities.