This study investigated changes in the average BMI of 5th and 6th grade elementary school students in Korea and provided foundational data to suggest the role of physical education for student health and set future directions. The 2019–2021 Physical Activity Promotion System (PAPS) of the Korean Ministry of Education was used. Data corresponding to 5th and 6th grade students (124,693 from 2019, 126,226 from 2020, and 117,809 from 2021) in 1,208 elementary schools in Korea were collected. The BMI was obtained by dividing weight by the square of height (㎏/m2). Repeated measures ANOVA was conducted for data analysis, and confidence intervals were modified through the Bonferroni correction for multiple comparisons. The Greenhouse-Geisser correction was used for effects test. The study findings are: First, the average BMI of 5th and 6th grade elementary school students in Korea increased significantly in 2021 compared to 2019 and 2020. Second, changes in the yearly average BMI showed a significant difference depending on gender and grade. Obesity among 5th and 6th grade elementary school students in Korea increased steadily in 2019–2021, which may be due to a decrease in students’ physical activity. Male students showed a steeper increase, regardless of grade.