Background: Children experience seasonal variations in growth whereby height increases most in spring and least in autumn, and weight increases least in spring and most in autumn. We hypothesized that activity restriction caused by efforts to contain the spread of coronavirus disease 2019 (COVID-19) would result in increased body mass index (BMI) in children, differing from conventional seasonal growth variations. Methods: We included 169 children who visited endocrine clinics of three hospitals in Korea at regular intervals under the same conditions for two years. Visit dates were D1 (January, 2019), D2 (July, 2019), D3 (January, 2020) before the COVID-19 outbreak, and D4 (July, 2020) during the pandemic. Differences in the z-score for height (HT), weight (WT), and BMI among time points and between spring seasons (i.e., S1–S3) were compared. Results: There were significant differences in BMIz among time points, which decreased from D1–D2 and increased from D2–D3 and D3–D4. WTz significantly increased from D2–D3 and D3–D4. BMIz values of S1 (spring 2019) and S3 (spring 2020) were −0.05 and 0.16, respectively, showing significant differences. WTz values between S1 and S3 were significantly different (−0.02 vs. 0.13). Conclusions: In 2019, there were conventional seasonal variations in BMIz, which declined in spring and increased in autumn, while in 2020, BMIz increased even in spring. The COVID-19 pandemic may have affected seasonal variations in the growth of children attending endocrine clinics.