Fluoride is present naturally in water and has been used worldwide for the prevention of caries. Several studies conducted in high water fluoride or endemic fluorosis areas reported that fluoride adversely affected children’s cognitive function, but some studies had negative findings. This study aimed to assess the relationship between urinary fluoride, dental fluorosis, and intelligence among schoolchildren living in communities with non-fluoridated drinking water. This cross-sectional study was conducted on 562 children aged 6–12 years in Taichung, Taiwan. Each child’s urinary fluoride level was determined by a fluoride-ion-selective electrode, and the dental fluorosis condition was evaluated according to the criteria of Dean’s Index. The Raven’s Colored Progressive Matrices-Parallel and Standard Progressive Matrices-Parallel were used to assess children’s intelligence. The results showed that the mean (±standard deviation) urinary fluoride concentrations were 0.40 ± 0.27 mg/L (0.43 ± 0.23 mg/g creatinine) among participants. The prevalence of dental fluorosis was 23.67%. After extensive evaluation of potential confounders, dental fluorosis and urinary fluoride were not associated with intelligence quotient (IQ) scores or grades in the regression models. In conclusion, dental fluorosis and urinary fluoride levels were not significantly related to the IQ of schoolchildren living in areas with low drinking water fluoride.