Long-term ingestion of large amounts of fluoride can lead to potentially severe skeletal problems and neurological consequences. This is an analytical cross sectional study conducted to evaluate the relationship between exposure to different drinking water fluoride levels and children's Intelligence Quotient (IQ) among school children in Nile East Locality-Sudan, convenient sampling strategy was utilized to include all the students aged 9–14 years presented on the day of examination from high and low fluoride areas. Sample of 197 school children from the two area were selected after fulfillment of inclusion criteria,( low fluoride area 89 and high fluoride area 108).Data collected by questionnaire and Raven's standard progressive matrices scale which was amended on Sudanese environment for assessment of Intelligence Quotient (IQ). Data was analyzed by using Statistical Packages for Social Sciences (SPSS) Appraisal of the Intelligence Quotient levels among the two groups (low and high-fluoride areas) showed a highly significant statistical association p value (0.001) the mean Intelligence Quotient in low fluoride area 95.02compering with high fluoride area 86.9. In comparison of the Intelligence Quotient scores of children in high and low area, only 1.1% of children were present in Grade 6 (definitely Excellent)in high fluoride area and 3.7% in low fluoride area. In addition, 5 (4.6%) in the low fluoride area in border line Intelligence Quotient in contrast to 17 (19.1%) in the high fluoride areas. Findings of the study concluded that the overall Intelligence Quotient levels in children's exposed to high fluoride level were significantly lower than the low fluoride areas and recommended that Further studies should be done to understand how toxic of fluoride can interfere with brain development.