Klinefelter syndrome (KS) is a sex chromosome disorder characterized by the presence of one or more extra X chromosomes. KS is well known by the common karyotype 47, XXY and presents as male infertility with hypogonadism in adults. Pediatric patients with KS commonly show neurodevelopmental disorders and cryptorchidism. We have reported a case of a 14-yr-old boy with KS and severe obesity (body mass index, 38.1 kg/m2), insulin (IRI) resistance (homeostatic model assessment 1 IRI resistance, 9.26), hyperlipidemia (serum low-density lipoprotein cholesterol level, 192 mg/dL; serum triglyceride level, 239 mg/dL), hypergonadotropic hypogonadism, and learning difficulties. The karyotype was 47, XXY, t(4;5) (q21.2;q32). Initially, he was unwilling to accept dietary restrictions and perform physical exercise against obesity. Testosterone replacement therapy was initiated at 16 years of age, which successfully improved the body composition, IRI resistance, and hyperlipidemia and increased the serum testosterone levels. Additionally, he adhered to recommendations for exercise and dietary restrictions. Patients with KS have risks of obesity and metabolic syndrome with sarcopenic conditions due to hypergonadotropic hypogonadism. Pediatricians should be aware of KS as a primary disease causing obesity. Testosterone replacement therapy could help ameliorate obesity and its comorbidities in patients with obesity and KS.