Few studies have examined the improving effects of exercise on the association between metabolites of impaired protein metabolism and insulin resistance in obese children. Therefore, this study aims to investigate the effect of circuit resistance training (CRT) on plasma levels of amino acids, alpha-hydroxybutyrate (α-HB), mannose, and urinary levels of glycine conjugated adducts in obese adolescent boys. Forty obese adolescent boys (body mass index above the 95th percentile) with an age range of 14-17 years were randomly divided into the CRT group ( = 20) and control group ( = 20). The CRT program (3 times/week, 70%-80% of 1-repetition maximum) was performed for 8 weeks. The results indicated that the body composition and plasma levels of glucose, insulin resistance, valine, mannose, lysine, and the sum of branched-chain amino acids (BCAA) were decreased because of CRT. The plasma levels of asparagine, glycine, serine, and urinary levels of glycine conjugated adduct also increased in the CRT group. Although α-HB level decreased during CRT, it had no significant difference from that of the control group. It can be concluded that the improvement in obesity complications including insulin resistance in obese adolescent boys after CRT may be due to decrease in plasma levels of mannose and BCAA and increase urinary metabolites. CRT improves glucose metabolism and insulin resistance in obese adolescent boys. CRT decreases plasma levels of mannose and BCAA and normalizes other amino acids. CRT increases urinary levels of glycine conjugated adducts.