Background: Youth spend a large amount of time in the school environment. Given the multiple influences of teachers, peers, and food and physical activity options, youth are likely to experience stressors that can influence their weight. This study examines the association between school climate and weight status. Method: Students (n = 28,582; 58 schools) completed an online, anonymous school climate survey as part of the Maryland Safe and Supportive Schools Project. Multilevel structural equation modeling was used to explore the association between school climate, personal stress, and obesity. Analyses were stratified by gender. Results: At the individual level, poor school climate (bullying, physical safety, and lack of whole‐school connectedness) was associated with an increased likelihood of being overweight among females (β = .115, p = .019) but not males (β = .138; p = .244), after controlling for age, race, and physical activity. There was no association between school climate at the school level and being overweight among males or females. A second model included stress as a potential mediator; stress attenuated the relationship between poor school‐related climate and being overweight (β = .039; p = .048) among females. Conclusion: Findings suggest that stress related to school climate can play a role in the health and weight status of youth.