Background: The current coronavirus disease 2019 (COVID-19) pandemic has health, social, and economic implications. Our primary objective was to evaluate changes in body mass index (BMI) from the pre-pandemic to COVID-19 pandemic period among a large pediatric population in Israel. Methods: This retrospective cohort study is based on data from Clalit Health Services, the largest health maintenance organization in Israel. The data accessed included sociodemographic, anthropometric, and clinical parameters of persons aged 2–20 years with at least one BMI measurement during 2017–2019 (pre-pandemic period) and one between April 1, 2020 and December 31, 2020 (pandemic period). Results: The cohort comprised 36,837 individuals (50.8% females); median age 11.2 years, 83.6% were Jewish and 10.3% of Arab ethnicity. BMI-SDS increased in both sexes (p < 0.001), in both ethnicities (p < 0.001), in all socioeconomic position clusters (p < 0.001), in children aged 2–18 years (P < 0.001), and in children with underweight or normal-weight in the pre-pandemic period (p < 0.001). For 21,610 individuals (35.6%), BMI-SDS increased ≥0.25 SD. The increase in BMI-SDS was greater in children aged 2–6 compared to 6.1–18 years; BMI-SDS decreased among those aged 18.1–20 years (P < 0.001). The increase in BMI-SDS was greater among those with underweight than normal weight; BMI-SDS decreased among those with overweight and obesity (P < 0.001). During the pandemic, overweight or obesity presented in 11.2% of those with normal weight in the pre-pandemic period; and obesity presented in 21.4% of those with overweight in the pre-pandemic period. Conclusions: The COVID-19 pandemic correlated with overall weight gain among children and adolescents, with the most substantial weight gain in children aged 2–6 years. Notably, the most significant increase in BMI-SDS was observed in children with underweight; BMI-SDS decreased in children with overweight and obesity. Policies should be established during the pandemic that focus on increasing physical activity, reducing sedentary time, and promoting healthy diets.