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Background: Adolescent behaviors and academic outcomes are thought to be shaped by school climate. We sought to identify longitudinal associations between school climate measures and downstream health and academic outcomes. Methods: Data from a longitudinal survey of public high school students in Los Angeles were analyzed. Eleventh-grade health and academic outcomes (dependent variables, eg, substance use, delinquency, risky sex, bullying, standardized exams, college matriculation), were modeled as a function of 10th-grade school climate measures (independent variables: institutional environment, student-teacher relationships, disciplinary style), controlling for baseline outcome measures and student/parental covariates. Results: The 1114 student respondents (87.8% retention), were 46% male, 90% Latinx, 87% born in the United States, and 40% native English speakers. Greater school order and teacher respect for students were associated with lower odds of multiple high risk behaviors including 30-day alcohol use (odds ratio [OR] 0.81; 95% confidence interval [CI] [0.72, 0.92] and OR 0.73; [0.62, 0.85]) and 30-day cannabis use (OR 0.74; [0.59, 0.91] and OR 0.76; [0.63, 0.92]). Neglectful disciplinary style was associated with multiple poor health and academic outcomes while permissive disciplinary style was associated with favorable academic outcomes. Implications for School Health Policy, Practice, and Equity: School health practitioners may prospectively leverage school environment, teacher-student relationships, and disciplinary style to promote health and learning. Conclusions: Our findings identify specific modifiable aspects of the school environment with critical implications for life course health.