Catalytic removal of the S-content from thiophene is a central step in efforts aiming to reduce the environmental burdens of transportation fuels. In this contribution, we investigate the hydrodesulfurization (HDS) mechanisms of thiophene (C4H4S) over γ-Mo2N catalyst by means of density functional theory (DFT) calculations. The thiophene molecule preferentially adsorbs in a flat mode over 3-fold fcc nitrogen hollow sites. The HDS mechanism may potentially proceed either unimolecularly (direct desulfurization) or via H-assisted reactions (hydrogenation). Due to a sizable activation barrier required for the first C–S bond scission of 54.6 kcal/mol, we predict that the direct desulfurization to contribute rather very insignificantly in the HDS mechanism. Transfer of adsorbed hydrogen atoms on the γ-Mo2N surface to the thiophene ring substantially reduces activation barrier required in the C–S bond scission to only 24.1 kcal/mol in a process that affords an adsorbed C4H6 * species and an S atom. Further hydrogenation of the unsaturated C4H6 * produces 2-butene. Kinetics and thermodynamics attributes dictate the occurrence of partial rather than full hydrogenation of C4H6 *. Calculated rate constants for all individual steps could be utilized to construct a robust kinetic model for the overall HDS process. Estimated conversion values of thiophene predict 50–70% consumption of thiophene at 700 K and low values of gas hourly space velocities. Reaction routes and kinetic parameters provided herein are useful to design stand-alone γ-Mo2N-based catalysts for applications entailing partial hydrogenation and hydrodesulfurization of severely contaminated S-fuels.