There is considerable research that suggests that school-based social-emotional programs can foster improved mental health and reduce problem behaviors for participating youth; in contrast, much less is known about the impact of these programs on physical health, even though some of these programs also include at least limited direct attention to promoting physical health behaviors. We examined the effects of one such program, Positive Action (PA), on physical health behaviors and body mass index (BMI), and tested for mediation of program effects through a measure of social-emotional and character development (SECD). Participating schools in the matched-pair, cluster-randomized trial were 14 low-performing K-8 Chicago Public Schools. We followed a cohort of students in each school from grades 3 to 8 (eight waves of data collection; 1,170 total students). Student self-reports of health behaviors served as the basis for measures of healthy eating and exercise, unhealthy eating, personal hygiene, consistent bedtime, and SECD. We collected height and weight measurements at endpoint to calculate age- and gender-adjusted BMI z-scores. Longitudinal multilevel modeling analyses revealed evidence of favorable program effects on personal hygiene (effect size [ES] = 0.48), healthy eating and exercise (ES = 0.21), and unhealthy eating (ES = −0.19); in addition, BMI z-scores were lower among students in PA schools at endpoint (ES = −0.21). Program effects were not moderated by either gender or student mobility. Longitudinal structural equation modeling demonstrated mediation through SECD for healthy eating and exercise, unhealthy eating, and personal hygiene. Findings suggest that a social-emotional and character development program without a primary focus on health behavior promotion can have a modest impact on outcomes in this domain during the childhood to adolescence transition.