Functional constipation negatively affects school-related quality of life for children and adolescents. We investigated the association between functional constipation, defined according to the Rome criteria version III, and dietary habits. The subjects of this cross-sectional study were 1,140 5th graders and 1,054 8th graders attending schools in Shunan City, Japan in 2012. Functional constipation was defined as having two or more symptoms of constipation. Dietary habits were assessed using a brief questionnaire. Self-reported biological, demographic and lifestyle information was obtained. Using multiple logistic models, dose-dependent associations among subgroups stratified with quintiles of nutrient and food intake were examined. The prevalence of functional constipation ranged from 3.7% to 8.3% across the grades. The most prevalent symptom was pain or hard stools. There was a link between higher rates of functional constipation and lower levels of dietary fiber intake, vegetables, and fruits ( p _trend=0.010-0.030). Associations with vegetables and fruits attenuated when controlling for dietary fiber intake ( p _trend=0.074-0.150). When 5th and 8th graders were separately analyzed, intake of dietary fiber, water from foods, and vegetables had beneficial effects on functional constipation in 8th graders ( p _trend=0.005-0.038), and fruit intake had a beneficial effect in 5th graders ( p _trend=0.012). Modification of dietary habits may have a positive effect in reducing functional constipation in school-age children. Diets rich in fiber, vegetables, and fruits, have the potential to improve functional constipation in Japanese children and adolescents.