BACKGROUND AND OBJECTIVES: Studies suggest that individual student-reported connection to school is associated with better mental health. However, there is less evidence for associations between schools' overall school climate and the mental health of their students. This may reflect limitations in which mental health outcomes have been examined. We conducted a large longitudinal study in schools, hypothesising that we would find associations at both the student and school levels between student-reported positive school climate, and reduced student conduct and emotional problems and improved mental wellbeing. METHODS: We tracked students in 20 English secondary schools from near the end of the first year of secondary school (age 11/12) over 3 years using reliable measures of school climate and mental health. RESULTS: We found associations between student-level reports of positive school climate at baseline, and reduced conduct and emotional problems and better mental wellbeing at 3-year follow-up adjusting for various potential confounders. We also found some evidence of adjusted associations between baseline school-level measures of overall positive climate and better student mental health at follow-up. However, these student- and school-level associations reduced considerably when also adjusting for baseline mental health. CONCLUSIONS: Our findings suggest that there are associations between school climate and student mental health at both the student and school level but these associations are complex and not necessarily causal.