Abstract Background There were some debates about the water fluoridation program in South Korea, even if the program had generally substantial effectiveness. Because the out-of-pocket expenditures for dental care were higher in South Korea than in other countries, an efficient solution was needed. Therefore, we examined the relationship between the implementation of water fluoridation and the utilization of dental care. Methods We used the National Health Insurance Service National Sample Cohort. In this study, data finally included 472,250 patients who were newly diagnosed with dental caries during 2003–2013. We performed survival analysis using cox proportional hazard model, negative binomial-regression, and regression analyses using generalized estimating equation models. Results There were 48.49 % outpatient dental care visit during study period. Individuals with water fluoridation had a lower risk of dental care visits (HR = 0.949, 95 % CI = 0.928–0.971). Among the individuals who experienced a dental care visit, those with water fluoridation program had a lower number of dental care visits (β = −0.029), and the period of water fluoridation had an inverse association with the dental care expenditures. Conclusion The implementation of water fluoridation programs and these periods are associated with reducing the utilization of dental health care. Considering these positive impacts, healthcare professionals must consider preventive strategies for activating water fluoridation programs, such as changes in public perception and relations, for the effective management of dental care in South Korea.