Since 1998, the authors have been working to improve the oral health of children at kindergartens and primary schools in the Kingdom of Tonga (Tonga). Our primary activity has been a school-based fluoride mouth-rinsing (FMR) program. FMR is performed using 7-10 mL of a 0.2% NaF solution for 1 min once per week at each school. In the present study, we evaluated the effect of school-based FMR on dental caries incidence among Tongan schoolchildren. A total of 109 children aged 10 years were evaluated at six primary schools on Tongatapu Island. The FMR group comprised 46 children who had participated in the school-based FMR program for at least 5 years 6 months; the control group comprised 63 children who had participated in the school-based FMR program for 1 year or less. During standardized dental examinations, decayed, missing, and filled teeth were counted by a single dentist at each school. The school-based FMR program effectively decreased the number of dental caries. A school-based FMR program may thus be very beneficial in preventing caries among children in Tonga.