The current computational study analyzes the oxidation reactions of the superoxide and hydroxyl radicals with cysteine residues due to their importance as natural targets to neutralize the harmful reactive oxygen species. Due to the high reactivity of the hydroxyl radicals with the surrounding environment, we also studied the oxidation reactions of organic radicals with cysteine. In addition, we explored the different reaction pathways between cysteine and the superoxide radicals in both anionic and protonated forms. All calculations were performed at the integrated quantum mechanical/molecular mechanical level in an explicit water box under periodic boundary conditions. Higher energy barriers were observed for the organic radicals than the hydroxyl radical, where the chemical nature of the organic radical and the branching pattern are the main factors contributing to the Gibbs energy barriers. The superoxide radical oxidation pathway exhibits a more complex nature due to the complicated interplay of various factors such as the underlying reaction mechanism, the involved oxidizing agent, the kinetic accessibility of the oxidation reaction, and the thermodynamics favorability of those oxidation reactions. We also examined the effect of the solvent-assisted hydrogen atom transfer on the different reaction barriers, which was found to be kinetically unfavorable.