There are few studies comparing adherence to Canadian 24-hour Movement Guidelines (24-h MG) before and during the COVID-19 pandemic and exploring the pandemic’s effect on childhood obesity. This survey-based 2-year study investigated changes in obesity and adherence to the 24-h MG in children before and during the COVID-19 pandemic. Data were collected at two points in time: pre-COVID-19 (May 2019; T1; n = 247) and during-COVID-19 (May 2021; T2; n = 171). Participants were healthy elementary school children aged between 6–12 years in northeastern Japan. The questionnaire comprised items on physical activity, screen time, sleep duration, adherence to the 24-h MG, and anthropometric and demographic characteristics. Among all participants, a statistically significant difference (p < 0.001) between the average body mass index at T1 (M = 16.06 kg/m2, SD = 2.08 kg/m2) and T2 (M = 18.01 kg/m2, SD = 3.21 kg/m2) was observed, where 17.8% were overweight and obese at T1 and 24% at T2, and 10.9% adhered to all 24 h MG at T1 and 4.1% at T2. To prevent obesity in children during the COVID-19 pandemic, environmental changes should be evaluated and appropriate preventive measures taken, including pro-community health programs that encourage parent-children outdoor activities.