Objectives: The aim of this study is to analyze the differences in factors related to the incidence of dental caries between children in fluoridated and non-fluoridated areas and compared the DMFT and DMFS scores to confirm the effect of water fluoridation program (WFP) in Geoje and Changwon. Methods: The oral health examination and questionnaire survey were conducted in fluoridated and nonfluoridated areas. The number of surveyed children aged 8, 10, and 12 years in the fluoridated and nonfluoridated area of two cities was 1,524 and 1,383, respectively. Self-recorded questionnaires included self-perception of their own dental health, daily toothbrushing frequency, intake frequency of cariogenic sweet snacks and beverages, experience of gingival bleeding, experience of unmet dental treatment, and use of oral hygiene device except for toothbrush and toothpaste. The prevalence of caries and fissure-sealant status were surveyed. The logistic regression analysis was used to analyze the difference in children’s self-rated oral health status between the fluoridated and non-fluoridated area. The mean number of sealed teeth and surfaces, marginal means of the DMFT and DMFS scores adjusted for the difference in the samples’ sex distribution, and region were compared between the fluoridated and nonfluoridated areas. Results: In the fluoridated area, the experience rate of unmet dental treatments was higher among children aged 10 years, intake frequency of cariogenic sweet snacks and beverages were higher among the whole sample, and experience rate of professional fluoride application were lower than in the nonfluoridated area. The DMFT score for permanent dentition adjusted for differences in sex, region, and mean number of fissure-sealed teeth in the fluoridated area was significantly lower among whole samples and 8-, 10-, and 12-year-olds alone than in the non-fluoridated area. Conclusions: WFP can alleviate oral health inequality because it is effective in reducing the incidence of caries among children is disadvantaged demographic, socioeconomic, and cultural contexts.