There have been numerous attempts to establish a correlation between obesity and stress, inflammatory, and dysmetabolism biomarkers in children and adolescents. Here, we performed a meta-analysis of existing studies to shed light on the elusive correlations of childhood and adolescent obesity with physiological indicators of stress, inflammation, and metabolism before and after lifestyle interventions. Observational studies, meta-analyses, narrative and systematic reviews were excluded. From a total of 53 articles, 11 were selected according to specific criteria. The biomarkers examined were circulating glucose, insulin, HDL, LDL, triglycerides, adiponectin, leptin, CRP, TNF-alpha, interleukin (IL)-6, systolic and diastolic blood pressure, and HOMA-IR. All analyses were performed using IBM SPSS Statistics Version 28.0.1.0 (142). The current meta-analysis provides evidence of a beneficial effect of a lifestyle intervention and/or drugs in children and adolescents living with obesity or overweight, consistent with a significant reduction in body fat—but not in BMI or waist circumference—an increase in circulating adiponectin and/or a reduction in serum insulin levels and diastolic blood pressure, and a trend towards a reduction of circulating leptin and glucose levels, as well as of the HOMA-IR. This meta-analysis indicates that lifestyle interventions could reduce overweight-/obesity-associated systemic inflammation and dysmetabolism even without an apparent decrease in BMI.