The roles of built-in thiol cofactors and the basic histidine (His) residues in the active site of mammalian thioredoxin reductases (TrxRs) are described with the help of experimental and density functional theory calculations on small-molecule model compounds. The reduction of selenenyl sulfides by thiols in selenoenzymes such as glutathione peroxidase (GPx) and TrxR is crucial for the regeneration of the active site. Experimental as well as theoretical studies were carried out with model selenenyl sulfides to probe their reactivity toward incoming thiols. We have shown that the nucleophilic attack of thiols takes place at the selenium center in the selenenyl sulfides. These thiol exchange reactions would hamper the regeneration of the active species selenol. Therefore, the basic His residues are expected to play crucial roles in the selenenyl sulfide state of TrxR. Our model study with internal amino groups in the selenenyl sulfide state reveals that the basic His residues may play important roles by deprotonating the thiol moiety in the selenenic acid state and by interacting with the sulfur atom in the selenenyl sulfide state to facilitate the nucleophilic attack of thiol at sulfur rather than at selenium, thereby generating the catalytically active species selenol. This model study also suggests that the enzyme may use the internal cysteines as cofactors to overcome the thiol exchange reactions.