Objective: To find the clinical and biochemical effects of high-intensity aerobic training with a high-protein diet in children with obesity following COVID-19 infection. Methods: By using the block randomization method, the eligible participants were randomized into two groups. The first group received high-intensity aerobic training with a high-protein diet (Group A; n = 38) and the second group were allowed to do regular physical activities and eat a regular diet (Group B; n = 38) for 8 weeks. Clinical (basal metabolic index (BMI) and muscle-mass-cross-sectional area (CSA)) and biochemical (Adiponectin, leptin, TNF-α, and IL-6) measures were measured at baseline, on the 8th week, and at 6-months follow-up. Results: Baseline demographic and clinical attributes show homogenous presentation among the study groups (p > 0.05). After eight weeks of intervention, and at the end of 6-months follow-up, the basal metabolic index (BMI) (6.3) (CI 95% 4.71 to 7.88), mid-arm CSA (17) (CI 95% 14.70 to 19.29), mid-thigh CSA (13.10) (CI 95% 10.60 to 15.59), mid-calf CSA (11.3) (CI 95% 9.30 to 13.29), adiponectin (−1.9) (CI 95% −2.13 to −1.66), leptin (5.64) (CI 95% 5.50 to 5.77), TNF-α (0.5) (CI 95% 0.42 to 0.57), and IL-6 (0.21) (CI 95% 0.18 to 0.23) showed more improvement (p < 0.001) in Group A than Group B (p > 0.05). Conclusion: Overall, this trial found that high-intensity aerobic training with a high-protein diet decreased the BMI percentile and muscle mass (arm, thigh, and calf), and positively altered the biochemical variables in children with obesity.