BACKGROUND: Children in rural areas are susceptible to zinc deficiency. Zinc deficiency in children can affect cognitive function in children. Zinc plays a role in cellular function and critical brain growth processes, including cell replication, DNA and RNA synthesis, and the release of neurotransmitters. AIM: This study aimed to analyze the condition of zinc deficiency and its relationship with the level of intelligence in children in rural areas. METHODS: The study design was cross-sectional, with a sample of 44 elementary school children aged 9–12 years taken randomly. Blood was drawn to measure serum Zn-levels, and serum Zn-levels were measured using Colorimetric Assay Kit (E-BC-K137). Zinc intake data were obtained from the food recall form, which was carried out 3 × 24 h. The level of intelligence is measured by the Culture Fair Intelligence Test method. The sample characteristics data obtained through a questionnaire. Furthermore, the data were analyzed using the Chi-square test. RESULTS: About 84.2% of children with insufficient zinc intake had low serum Zn-levels. There was a significant relationship between zinc intake and serum zinc levels (p = 0.026; PR = 4.293). Children with low serum zinc levels of 96.5% have intelligence levels below average. There was a significant relationship between serum zinc levels and intelligence level as well (p = 0.001; PR = 24,500). CONCLUSION: Zinc deficiency in children is characterized by low serum Zn-levels. Low serum Zn-level is caused by low zinc intake, thus children with low serum Zn-levels are at risk of having intelligence level below average. Therefore, health education about the importance of zinc intake in children should be given to parents, so that the incidence of zinc deficiency in children can be reduced.