Background Obesity in children is a public health concern in Japan. To evaluate the current state of the obesity problem and inform future directions, we aimed to provide an updated account of secular trends in the percentage of overweight (POW) children by gender and school grade, and evaluate changes in POW after participation in the obesity health screening. Methods The current study utilized aggregated data from the Setagaya Ward, Tokyo, public elementary and middle school populations from 2009 to 2018. Data on the percentage of overweight >= 30% (POW-30) and percentage of abnormal blood test results were examined by year, gender, and school grade level. Individual-level data from 2015 to 2017 in children who participated in a follow-up obesity health screening were evaluated for changes in median POW. Results A decreasing trend in students with a POW-30 was observed from 2009 to 2011, with rates stabilizing thereafter. The highest proportions of POW-30 were observed in 2010 (4.8% in middle school boys; 2.8% in middle school girls). From third grade, the difference in percentage by gender appeared to get increasingly larger until the beginning of middle school. Among obesity health screening participants, abnormal blood tests for total cholesterol and triglycerides showed a slightly increasing trend over time, and changes in POW after screening were greatest for middle school students. Conclusions Increases in obesity were not observed in Setagaya Ward public school students since 2010, but disparities exist by gender and grade level, suggesting that tailored intervention strategies may be useful to optimize aspects of the obesity health screening program.