Despite legal safeguards, the Yanomami community faces challenges such as unauthorized incursions by gold miners, resulting in environmental degradation, particularly from mercury. This jeopardizes the health and food security of indigenous individuals, especially due to the consumption of contaminated fish. Ethnic and racial disparities persist in indigenous healthcare, marked by troubling health indicators such as malnutrition, anemia, and infectious diseases. This cross-sectional study, conducted in October 2022 in the Yanomami Indigenous Territory in the Amazon Forest, Brazil, presented clinical, laboratory, and neurodevelopmental findings in Yanomami children chronically exposed to methylmercury. The results revealed that Yanomami children exhibited weights and heights below expectations (median Z-scores of −1.855 for weight for age and −2.7 for height for age), a high prevalence of anemia (25%), low vaccination coverage (15%), and low IQ (average 68.6). The Total Hair Mercury (Total Hg) levels ranged from 0.16 µg/g to 10.20 µg/g (mean: 3.30 µg/g; median: 3.70 µg/g). Of 117 children tested, 93 children (79.4%) had levels ≥ 2.0 µg/g (had no significant difference between sex). Among the 58 children for whom it was possible to estimate the Total Intelligence Quotient (TIQ), the average value was 68.6, ranging from 42 to 92 points (median: 69.5; standard deviation: 10.5). Additionally, the lowest score on the IQ test was associated with 5 times the risk of having high levels of mercury in their hair, 2,5 fold the risk of having an older age, and almost 8 times the risk of consuming fish, adjusting for nut consumption. Notwithstanding the study’s limitations, results suggest that mercury contamination from illegal mining activities on indigenous lands may negatively impact neurodevelopment in older indigenous children, particularly those fish consumers, despite the inherent benefits of fish consumption. Addressing other socio-environmental concerns is crucial for enhancing the overall health of the population.