Periodic ab initio DFT calculations based on ultrasoft pseudopotentials and a plane-wave basis set were carried out to shed some light on the adsorption and reaction mechanisms of thiophene over vanadium carbide and vanadium nitride cubic face-centered (001) surfaces and its implications for hydrodesulfurization (HDS). Direct (DDS) and hydrogenating (HYD) routes were considered for further desulfurization reactions. Furthermore, to identify their role in the adsorption and desulfurization process, various initial configurations for the adsorption complexes were investigated. Our results suggest that ring hydrogenation does not necessarily lead to a preference for the HYD pathway of thiophene desulfurization. Moreover, surface and electronic effects due to adsorption were also evaluated. We have found that under ideal conditions, vanadium nitride and carbide surfaces present similar activity over desulfurization of thiophene, in qualitative agreement with experiments.