Objectives Nutrition during the first 3 years of life is critical to neurodevelopment. Native populations experience poverty, inequality, and food insecurity. Therefore, we analyzed the relationship between feeding during infancy and cognitive performance in schoolchildren of rural indigenous communities in Riobamba, Ecuador. Methods Thirty‐seven schoolchildren (5–6 years) were recruited. We determined duration of exclusive breastfeeding, weaning age, age of cow's milk incorporation, daily intake of cow's milk, age of solid and liquid incorporation, and sociocultural and anthropometric parameters. Verbal, manipulative, and total intelligence quotients were evaluated with Wechsler Preschool and Primary Scale of Intelligence. Results Means of verbal, manipulative, and total intelligence quotient scores were 86.46 ± 11.55, 96.39 ± 9.96, and 89.25 ± 10.43, respectively. Children were exclusively breastfed until 6.83 ± 3.97 months and weaned at 17.17 ± 5.58 months. Age of cow's milk incorporation was 12.58 ± 6.06 months, with a daily intake of 737.50 ± 417.50 mL. Solids were incorporated at 10.11 ± 4.43 months and liquids at 7.72 ± 3.30 months. Positive associations between duration of exclusive breastfeeding and manipulative (unadjusted: ρ = .545, P = .006; r = .491, P = .028; adjusted for children's body mass index, and ethnicity and educational level of mothers: r = .522, P = .041) and total (unadjusted: ρ = .483, P = .017; adjusted: r = .572, P = .036) intelligence quotients were found. Frequency of children with manipulative (χ2[2] = 7.093, P = .029) and total (χ2[2] = 7.198, P = .027) intelligence quotient ≥90 was higher in those exclusively breastfed >6 months. Furthermore, schoolchildren in the >6 months group had better manipulative (101.75 ± 9.08 vs 89.71 ± 8.56, P = .038) and total (94.50 ± 11.89 vs 84.86 ± 5.05, P = .036) intelligence quotient than those in the <6 months group, independent of anthropometric and sociocultural factors. Conclusions Longer exclusive breastfeeding was related to better total intelligence quotient in rural indigenous schoolchildren.