The goal of the present study was to compare the influence of the methylation capacity of arsenic, as well as insulin resistance on psychological characteristics of school students from elementary and junior high school. 296 elementary and 318 junior high school students participated in health examinations, completed questionnaires and determined their concentrations of urinary arsenic species and psychological characteristics. Insulin resistance was determined by means of the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). We found that HOMA-IR values were significantly related to increased score of the depression and anger after adjusted for age, gender, schools, father's educational levels, mother's educational levels, BMI, body fat, and urinary creatinine in all students. Anxiety scores and depression scores of junior high school children were significantly higher compared to elementary school children, but lower in disruptive behavior scores. HOMA-IR levels were significantly inversely related to self-concept scores in junior high school students. A greater urinary inorganic arsenic percentage (iAs%) was marginally significantly related to a higher depression score in junior high school students. This is the first study to show a relationship between HOMA-IR levels or urinary arsenic profiles and psychological distress in school students from elementary and junior high school.