Neighborhood characteristics are thought to be associated with adolescent health and behavior. However, there have been very few population-based surveys using data from individual responses living in the same school district area. Tokyo TEEN Cohort data, collected from three Tokyo municipalities, were used to examine the association between psychological symptoms in school districts during early adolescence (age 10) and later psycho-behavioral conditions in adolescents (ages 12 and 14). Hierarchical linear models showed that school district-level depressive symptoms, psychological well-being, and prosocial behaviors at age 10 were associated with the corresponding individual-level indices at age 12, after controlling for demographic characteristics and baseline individual scores as covariates. Furthermore, School district-level behavioral problems at age 10 were associated with individual-level indices at ages 12 and 14. These results suggest that school district environments in which young adolescents grow up influence adolescents’ development and well-being.