Background Oral health problems especially dental caries are common in school children, and education programs may help to prevent these conditions. The aim of current study was to examine the effects of an educational program based on a Health Belief Model (HBM) to improve oral health behaviors of elementary school children. Methods A total of 112 children ages 6–12 years old accompanied by one of their parents were randomly assigned to intervention/test and control groups. In the intervention group, five consecutive weekly educational sessions based on the HBM were provided, while the control group received only routine education delivered by the dental clinic. The Decayed, Missing, and Filled Teeth (DMFT) score, papillary bleeding index, and responses to the HBM questionnaire were assessed in the intervention and control groups at baseline and three-month follow-up after the intervention was completed. Within-group and between-group differences were examined using the Student’s t-test and analysis of covariance. Results All HBM domains were improved at follow-up in the intervention group compared to the control group (p < 0.001). The largest change was in perceived susceptibility, whereas the smallest changes were in perceived severity and perceived benefits. The papillary bleeding index demonstrated a significant change from baseline to follow-up in the intervention group (reduction of 0.7, 95% CI = − 0.9 to − 0.5). All components of the DMFT score except missing teeth also improved in the intervention group compared to controls. However, no significant difference was found in total DMFT score between intervention and control groups. Conclusion An education program based on HBM may be more effective than current methods used to educate children and their parents on optimal oral health behaviors. Administration of interventions of this type along with other school-based programs to prevent dental caries may be helpful in grade-school children.