Background: The purpose of this study was to assess the effect of a school-based nutrition program using a cafeteria environment intervention and classroom nutrition education on self-reported fruit and vegetable (FV) consumption, self-efficacy to select FV, and preference for healthy foods. Methods: Using quasi-experimental pre-post design with 3 study conditions, a total of 665 fourth- and fifth-grade students participated in the study. The comprehensive intervention included a behavioral economics cafeteria intervention and weekly classroom nutrition education for 1 academic year. The intervention was designed and delivered by the extension system. Results: The comprehensive group showed significant improvement in some indicators including eating vegetables for lunch (p = 0.007), number of days eating vegetables (p < 0.001) and fruits (p < 0.001) in the last week, and self-efficacy in preparing FV at home (p = 0.034) compared to the control and cafeteria groups. Food preference of some food items, including oatmeal (p = 0.036 for cafeteria group, p < 0.001 for comprehensive group), whole grain noodles (p = 0.011 for comprehensive group), and vegetables (p = 0.003 for comprehensive group), significantly improved in the cafeteria and/or comprehensive group. Conclusions: Classroom nutrition education combined with cafeteria improvement has the potential to improve diet-related behavior of elementary school children. Also, collaborative partnership between schools and extension can enhance program sustainability.