School climates are important for children's socioemotional development and may also serve as protective factors in the context of adversity. Nevertheless, little is known about the potential neural mechanisms of such associations, as there has been limited research concerning the relation between school climate and brain structure, particularly for brain regions relevant for mental health and socioemotional functioning. Moreover, it remains unclear whether the role of school climate differs depending on children's socioeconomic status. We addressed these questions in baseline data for 9- to 10-year-olds from the Adolescent Brain and Cognitive Development study (analytic sample for socioemotional outcomes, n = 8887), conducted at 21 sites across the United States. Cortical thickness, cortical surface area, and subcortical volume were derived from T1-weighted brain magnetic resonance imaging. School climate was measured by youth report, and socioemotional functioning was measured by both youth and parent report. A positive school climate and higher family income were associated with lower internalizing and externalizing symptoms, with no evidence of moderation. There were no associations between school climate and cortical thickness or subcortical volume, although family income was positively associated with hippocampal volume. For cortical surface area, however, there was both a positive association with family income and moderation: There was an interaction between school climate and income for total cortical surface area and locally in the lateral orbitofrontal cortex. In all cases, there was an unexpected negative association between school climate and cortical surface area in the lower-income group. Consequently, although the school climate appears to be related to better socioemotional function for all youth, findings suggest that the association between a positive school environment and brain structure only emerges in the context of socioeconomic stress and adversity. Longitudinal data are needed to understand the role of these neural differences in socioemotional functioning over time.