Background: Childhood obesity is a public health problem worldwide. There is convincing evidence that school-based interventions are effective in managing childhood obesity. However, the nature of interventions, its impact on prevention of obesity and how they work remain poorly understood. The primary objective of this study was to examine the impact of a multicomponent lifestyle intervention on weight and body mass index (BMI) of children in a school-based setting. Methods: It is a cluster randomized trial where four schools were randomly selected and allocated to intervention and control arm equally. Of the 462 schoolchildren selected, 201 were assigned to the intervention group and 261 belonged to the control group. Children in the intervention arm received a multicomponent lifestyle package. Primary outcome measures included anthropometric measurements (weight, BMI, skinfold thickness and waist and hip circumference), whereas secondary outcomes were biochemical parameters, physical activity and dietary intake. Results: Compared with controls and adjusting for age, sex and clustering within classes, children in the intervention group showed decrease in the weight by − 0.08 (−0.15 to − 0.00, p = 0.048) z-score units, waist circumference by − 0.14 (−0.25 to − 0.03, p = 0.01) and triceps thickness by − 0.35 (−0.47 to − 0.22, p < 0.001) z-score units; however, BMI showed no significant decrease. There was significant reduction in intake of energy, protein and fat but no to minimal reduction in biochemical parameters. Conclusion: A school-based lifestyle intervention package favorably affected anthropometric (weight, waist circumference and triceps and biceps thickness) and behavioral parameters. At least 20 weeks of healthy lifestyle promoting intervention package should be included in school curriculum in each academic year for sustainable impact and behavioral change to reduce the burden of lifestyle disorders.