In Japan, comprehensive food education (shokuiku) programs are carried out with the aim of improving dietary practices and thereby reducing the incidence of lifestyle-related diseases, including dental caries. The purpose of this prospective cohort study was to investigate the association between knowledge about shokuiku and the increase in dental caries among Japanese university students who had attended a shokuiku program while in junior/senior high school. A total of 562 students volunteered to undergo oral examinations over a three-year follow-up period, during which the number of cases of dental caries were recorded. Additional information was collected using a questionnaire survey regarding knowledge about shokuiku, dietary habits, and oral health behaviors. In logistic regression analysis, males who lacked knowledge about shokuiku had significantly higher odds for dental caries than those who did not (odds ratio (OR), 2.00; 95% confidence interval (CI), 1.12-3.58; p = 0.019). On the other hand, among females, those who frequently consumed sugar-sweetened soft drinks had significantly higher odds for dental caries than those who did not (OR, 1.89; 95% CI, 1.05-3.42; p = 0.035). These results suggest that having no knowledge about shokuiku is associated with a risk of increase in dental caries in Japanese male university students.