Environmental influence on intelligence quotient (IQ) is poorly understood in developing countries. We conducted the first cross-sectional investigation to assess the role of socio-economic and environmental factors on schoolchildren’s IQ in Jalalabad, Afghanistan. A representative sample of 245 schoolchildren aged 7–15 was randomly selected in five schools. Children’s records included: non-verbal IQ TONI-1 scale, body mass index, socio-economic status, and further environmental indicators (water supply, proximity to a heavy-traffic road, use of surma traditional cosmetics). The mean age of the children was 11.7 years old (±2.0 years), and 70.2% and 29.8% were male and female, respectively. The children’s mean IQ was 83.8 (±12.6). In total, 37 (14.9%) of the children were overweight, 78 (31.5%) were living below the USD 1.25 poverty line, 133 (53.6%) used tap water supply, 76 (30.6%) used surma, and 166 (66.9%) were exposed to heavy road traffic. The children’s IQ was significantly and independently lowered by tap water use (−3.9; 95% CI [−7.1; −0.6]) and by aging (−1.4; 95% CI [−2.2; −0.6]), as revealed in multivariate analysis, independently of gender, socio-economic status, exposure to heavy road traffic, overweight status, and surma use. Lower IQ among older children is possibly attributed to chronic stress experienced by adolescents due to living conditions in Afghanistan. While using tap water prevents fecal peril, it may expose children to toxic elements such as lead which is known to lower their intellectual development.