There is an ongoing debate whether early exposure to fluoride is necessary. The effect of early exposure to fluoride needs to be understood to inform the appropriate population oral health policy. This study aimed to evaluate the effects of systemic fluoride intake in early childhood on caries experience of the permanent dentition observed at the age of 8 or 9 years, controlling for the effects of topical exposures to fluoride at the age of 5 years. The fluorosis experience of children was used as a proxy indicator for early exposure to fluoride, while exposures to fluoride at the age of 5 years, which were collected retrospectively, were used to control for the topical effect on permanent caries experience of the same children. Caries experience recorded at 8 or 9 years of age of 571 children was compared between groups with or without fluorosis. Bivariate analysis and multivariate analysis controlling for exposures to fluoride at the age of 5 years and other potential contributory factors were conducted. A quarter of the sample had very mild to mild fluorosis, while 15% had caries experience in the permanent dentition. Multivariate models showed that children who did not have fluorosis had a higher prevalence and severity of caries compared to those with fluorosis after controlling for other factors. In conclusion, there was a significant negative association between fluorosis status and caries experience in the permanent dentition.