This study analyzes the role of education in the outcomes of the reform of the Japanese annual health checkup program. In April 2008, the annual checkup was redesigned to address concerns about metabolic syndrome. As the checkup is mandatory only for salaried workers, their participation rate is significantly higher than other workers; thus, they were most affected by the reform. Using institutional information, a difference-in-differences estimation was conducted with salaried workers as the treatment group and self-employed workers as the control group. We found that the reform caused significant changes in health behaviors and outcomes only among university graduates who were at a relatively high risk of metabolic syndrome. This highly educated group increased their physical activity, brought energy intake close to an ideal level, and achieved significant weight loss and BMI reduction to levels that minimize all-cause mortality among middle-aged Japanese. A secondary analysis implies that the difference in cognitive functioning test scores may be a critical factor in explaining the heterogeneous responses to the reform, suggesting that thoroughly well-articulated recommendations for healthy behaviors are needed in order to improve reform uptake.