Abstract Background Educational policies may have a substantial impact on health and well-being of students, who spend most of their daily lives at school. Policies on secondary education in Korea has changed in the late 2000s, which diversified college entrance exams (CEEs) and made the National Curriculum (NC) more autonomous to mitigate students’ burden of preparing for CEEs. This study aimed to estimate effects of educational policy changes on unhappiness, which is known to be associated with health status such as mortality, morbidity, and prognosis, of students in secondary education. Methods Using repeated cross-sectional self-reported data of 773,362 students in the Korea Youth Risk Behavior Web-based Survey during 2006-2016, cross-classified random effects models were fitted to estimate the fixed cohort effects of educational policy changes on unhappiness while considering individual factors and random effects of periods and grade cohorts. Results Students’ unhappiness increased when the NC began to become autonomous (odds ratio [OR] 1.21, 95% confidence interval [CI] 1.03-1.42), but it increased less after the autonomous NC was fully applied (OR 1.14, 95% CI 0.92-1.42). Two times of diversification of CEEs increased unhappiness (OR 1.21, 95% CI 1.06-1.38 for the first diversification and OR 1.33, 95% CI 1.07-1.67 for the second diversification). Unhappiness was high in students with high stress level (OR 7.59, 95% CI 7.43-7.75), low academic performance (OR 1.48, 95% CI 1.44-1.52), and low household economic status (OR 2.32, 95% CI 2.26-2.39). Conclusions Enhancement of autonomy of the NC and diversification of CEEs increased students’ unhappiness. Educational policy changes that diversified competencies required for college admission might result in an increase in academic burden in the context of Korea, where entrance into prestigious universities is crucial for success in life. Improvement of educational policy is needed to increase students’ happiness. Key messages Educational policies may have a substantial impact on health and well-being of students, who spend most of their daily lives at school. Education policy changes in Korea increased students’ unhappiness, which might be due to an increase in academic burden resulted from diversification of competencies required for college admission.