The objective of this study is to analyze the impact of innovative school policies and innovative policy on student agency, while also differentiating between various types of school courses. This study employs data from the initial phase of the longitudinal investigation of the Incheon Gyeoldaerojaram school. The investigation utilized both a multilevel model and a latent profile model. The findings of the analysis indicate that student agency expands as pupils go from elementary school to middle school or high school. While the Gyeoldaerojaram school itself did not directly impact student agency, the static innovation climate of the school did have an effect on student agency. Furthermore, when student agency was categorized into three distinct subfactors, namely autonomy, responsibility, and competence, the prevalence of student agency was found to be greater in both elementary and high schools. The prevalence of academic underperformance was greater in primary schools and even more in secondary schools. Based on the above findings, we examined the policy implications of innovative schools and student agency.