Insulin resistance is a key characteristic of metabolic syndrome (MetS). The hepatic nuclear factor- κB (NF-κB) signaling pathway plays a crucial role in insulin resistance and the development of type 2 diabetes. Our study aimed to examine the impact of cysteine (Cys) on various biochemical and histopathological parameters in the liver and kidney, hepatic NF-kβ expression, oxidative stress, inflammation, glycation, carbonyl stress markers, and insulin resistance. The study involved four groups of rats, each consisting of seven rats: a control group, a MetS group, and two similar groups receiving Cys treatment. Metabolic syndrome was induced in rats by administering a 40% sucrose solution, while, the treated groups received 50 mg/L Cys in their drinking water. Various factors, including body weight, hepatic NF-kβ expression, levels of antioxidants, anti-glycation, oxidative stress, carbonyl stress, inflammatory, anti-glycation, and glycation markers were assessed in blood and tissues. Liver and kidney function parameters and metabolic profiles were measured. Finally, liver tissue was also evaluated by a pathologist. The results showed that Cys reduced hepatic NF-kβ expression, oxidative stress, inflammation, glycation and carbonyl stress markers, as well as liver fatty content, blood sugar levels, insulin resistance, cardiovascular risk index, and body weight. The treatment also mitigated histopathological liver changes and acute hepatitis (p < 0.001). Cysteine exhibited anti-obesity and anti-atherosclerotic effects, improved β-cell function, insulin sensitivity, and lipid metabolism, and enhanced liver and kidney function, as well as prevented acute hepatitis by restoring the GSH/GSSG ratio, hepatic NF-kβ signaling, and carbonyl stress.