Background: The coronavirus disease pandemic is predicted to have adverse health effects on children and adolescents who are overweight or obese due to restricted school activity and stay-at-home orders. The purpose of this observational study was to determine the factors associated with weight gain in children and adolescents with overweight and obesity during coronavirus disease 2019 (COVID-19) lockdown. Methods: Ninety-seven participants (sex- and age-specific body mass index (BMI) ≥ 85th percentile) were included. A baseline examination was conducted pre-COVID-19 (August 2019 to January 2020), and re-examination was performed post-lockdown (June to September 2020) and the results were compared. Correlation and regression analyses were conducted to investigate the association among changes in cardiometabolic markers and lifestyle behaviors with changes in BMI z-score. Results: During the COVID-19 pandemic, an increase in BMI z-score (2.56 [2.01–2.94] to 2.62 [2.03–3.18]) was noticed in children and adolescents with obesity. Changes in cardiometabolic markers including liver enzymes, triglycerides (r = 0.398), leptin (r = 0.578), and adiponectin (r = −0.326), as well as muscular strength (r = −0.212), were correlated with the increase in BMI z-score. According to a multivariate regression analysis, changes in sedentary time (B = 0.016; 95% confidence interval [CI], 0.001–0.032) and fast-food consumption (B = 0.067; 95% CI, 0.013–0.122) were the lifestyle variables associated with BMI z-score increase. Conclusion Changes in lifestyle behaviors including fast-food consumption and sedentary time during the COVID-19 pandemic may be associated with weight gain. In order to prevent health-related risks in children and adolescents with obesity during the pandemic, it is important to maintain the level of physical activity and healthy dietary habits.