Childhood obesity is an increasing health care problem associated with insulin resistance and low-level systemic inflammation, which can ultimately lead to diabetes. Evidence for efficacy of therapeutic intervention programs on the early development of obesity associated sequelae is moderate. This paper investigates the effect of a multidisciplinary short-term intervention program on insulin resistance and metaflammation in childhood obesity. Two hundred and 36 overweight or obese children and adolescents between the ages of 10 and 14 were included in a prospective 5 months intervention study, which included sports, psychotherapy, and nutritional counseling. Primary endpoints were the effects on body mass index standard deviation score (BMI-SDS) and homeostatic model assessment of insulin resistance (HOMA-IR), key secondary endpoints were the levels of C-reactive protein (CRP), leptin, and adiponectin. At baseline, a substantial proportion of participants showed signs of insulin resistance (mean HOMA-IR 5.5 ± 3.4) despite not meeting the diagnostic criteria for diabetes, and low-level inflammation (mean CRP 3.9 mg/l ± 3.8 mg/l). One hundred and 95 participants (83%) completed the program resulting in a significant reduction in BMI-SDS, HOMA-IR, CRP, and leptin and a significant increase in adiponectin (mean change compared to baseline −0.14, −0.85, −1.0 mg/l, −2.8 ng/ml, and 0.5 µg/ml, respectively; p < 0.001 each). Effects on BMI-SDS, HOMA-IR, CRP, and adiponectin were largely independent whereas leptin was positively correlated with BMI-SDS and total fat mass before and after intervention (r = 0.56 and 0.61, p < 0.001 each). Short-term multidisciplinary intervention successfully Mayerhofer et al. Insulin Resistance in Childhood Obesity improved body composition, insulin sensitivity, low-level systemic inflammation, and the adipokine profile in childhood obesity. Our findings highlight the immediate connection between obesity and the pathophysiology of its sequelae, and emphasize the importance of early intervention. Continued lifestyle modification is likely necessary to consolidate and augment the long-term effects.