Improving children's nutrition and physical activity have become priorities in the United States. This quasi-experimental study evaluated the longitudinal effects of a 3-year, school-based, health promotion intervention (i.e. nutrition and physical education, classroom physical activity, professional development and health promotion for teachers and families, and strengthening wellness policies and family/community partnerships) on children's health behaviors in four, rural, low-socioeconomic status elementary schools. A total of 999 kindergarten to third-grade children participated in data collection consisting of 4-day pedometer tracking and previous-day fruits and vegetables consumption recall from baseline in January, 2011 through 12 follow-up assessments ending May, 2013. The mixed-effects regression models showed that children's nutrition and physical activity behaviors significantly improved over the 3-year intervention. The percentages of children who met the nutrition recommendation increased from 11 to 23% for girls and 12 to 23% for boys, while the percent who met the physical activity recommendation increased from 1 to 16% for girls and 3 to 7% for boys. Further, children's age and their school impacted certain intervention effects. This school-based intervention could be disseminated to promote healthy behaviors among rural disadvantaged children. Engaging parents and community partnerships is recommended to expand the traditional, children-focused education interventions.