Background: The COVID-19 pandemic has imposed significant changes on daily life. It negatively impacts children’s physical activity and lifestyle behaviors, which may cause accelerated weight gain during the COVID-19 pandemic. This study aims to evaluate children’s longitudinal age- and sex-adjusted body mass index (BMI) percentile changes during and after the COVID-19 pandemic. Methods: Height and weight data were obtained from electronic medical records for children (ages 2–18) visiting outpatient clinics during three periods: pre-COVID-19 lockdown, during COVID-19 lockdown, and post-COVID-19 lockdown. According to the availability of anthropometric information, three partially overlapping cohorts were formed: Cohort 1 (N = 934, pre- and during lockdown), Cohort 2 (N = 1129, during and post-lockdown), and Cohort 3 (N = 203, data from all three periods). Results: During the lockdown, the mean changes in percentiles of age- and sex-adjusted BMI were 6% ± 0.23, while after the lockdown, there were smaller mean changes in BMI percentiles (1% ± 0.19). There were significant associations of age and the baseline BMI categories with the change in the means of the adjusted BMI percentile of children during and after the COVID-19 pandemic (p-value < 0.001). In addition, there were significant associations of gender and the baseline BMI categories with the change in the means of the adjusted BMI percentile of children over a three-time series (p-value: <0.04, <0.001, respectively). Conclusions: In conclusion, children experienced increased BMI during and after the COVID-19 lockdown. This result highlights the importance of structured interventions to mitigate the consequences during challenging times on children’s health.