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The COVID-19 outbreak led to widespread school closures and the shift to remote teaching, potentially resulting in lasting negative impacts on teachers’ psychological well-being due to increased workloads and a perceived lack of administrative support. Despite the significance of these challenges, few studies have delved into the long-term effects of perceived instructional leadership on teachers’ psychological health. To bridge this research gap, we utilized longitudinal data from 927 primary and secondary school teachers surveyed in two phases: Time 1 in mid-November 2021 and Time 2 in early January 2022. Using hierarchical linear modeling (HLM), our findings revealed that perceptions of instructional leadership, especially the "perceived school neglect of teaching autonomy" at Time 1 were positively correlated with burnout levels at Time 2. Additionally, burnout at Time 2 was positively associated with psychological distress and acted as a mediator between the "perceived school neglect of teaching autonomy" and psychological distress. In light of these findings, we recommend that schools prioritize teachers’ teaching autonomy and take proactive measures to mitigate burnout and psychological distress, aiming for the sustainable well-being of both teachers and students in the post-pandemic era.