NRH:quinone oxidoreductase 2 (NQO2) is a flavoenzyme that catalyzes a one-step two-electron reduction of quinones. During this enzyme catalysis, the 7,8-dimethyl isoalloxazine (flavin) ring of the enzyme-bound cofactor, flavin adenine dinucleotide (FAD), shuttles between reduced and oxidized states as the enzyme passes through multiple cycles of binding/release of alternate substrates. These redox changes in NQO2, however, lead to unequal charge separation between the flavin ring and the active site, which must be stabilized by reorganization of the surrounding protein matrix. In this study, we have used a combined quantum mechanical/molecular mechanical method to simulate the electron and proton addition reactions of the flavin-bound NQO2. We have computed the redox potentials and pK(a)'s of the enzyme-bound flavin. The present work demonstrates that upon reduction, the NQO2 active site stabilizes the flavin anionic hydroquinone state. Simulation data has also allowed quantitative estimation of the electrostatic contributions of active site residues. Their significance in oscillatory redox transition of this flavoenzyme is discussed.