Background <p>This study aims to evaluate the effects of an NGO (Non-Governmental Organization) -supported school-based oral health promotion program in primary schools of Iran.</p> Methods and materials <p>This oral health-promoting program was conducted by the Barekat Organization (an NGO that supports the construction and equipment of schools in deprived regions) in cooperation with the Ministries of Education and Health and Medical Education in 2022. The program covered 3,000 schoolchildren in 32 schools. It included the education of schoolchildren, their parents, and their teachers using printed worksheets, face-to-face educations, and holding workshops by the school health educators from September 2022 to May 2023. The total mean score and the mean scores of sub-domains for students’ knowledge were compared using paired t-test after 9 months (α = 0.05).</p> Results <p>The data of 576 schoolchildren including 261 (43.5%) boys and 315 girls (56.5%) were selected randomly for analysis. The total knowledge was improved significantly (from 9.1 ± 2.9 to 13.5 ± 3.1; <i>p</i> &lt; 0.001; Cohen Effect Size = 1.4). At the baseline, female students had a higher baseline knowledge significantly (<i>p</i> = 0.001). The mean scores of knowledges increased in both genders after the interventions (<i>p</i>-value &lt; 0.001). The most significant changes were observed regarding the knowledge of tooth eruption and tooth brushing, whereas the least significant changes were noticed in the healthy diet domains.</p> Conclusion <p>Educational interventions provided in primary schools proved to be effective in improving schoolchildren’s knowledge. Therefore, the findings can be considered convincing evidence for the implementation of a model for successful cooperation between the Ministry of Health and Medical Education and NGOs.</p>