Purpose As impaired glucose metabolism may arise progressively during childhood, we sought to determine whether the introduction of specialist-taught school physical education (PE) based on sound educational principles could improve insulin resistance (IR) in elementary school children. Methods In this 4-yr cluster-randomized intervention study, participants were 367 boys and 341 girls (mean age = 8.1 yr, SD = 0.35) initially in grade 2 in 29 elementary schools situated in suburbs of similar socioeconomic status. In 13 schools, 100 min·wk−1 of PE, usually conducted by general classroom teachers, was replaced with two classes per week taught by visiting specialist PE teachers; the remaining schools formed the control group. Teacher and pupil behavior were recorded, and measurements in grades 2, 4, and 6 included fasting blood glucose and insulin to calculate the homeostatic model of IR, percent body fat, physical activity, fitness, and pubertal development. Results On average, the intervention PE classes included more fitness work than the control PE classes (7 vs 1 min, P < 0.001) and more moderate physical activity (17 vs 10 min, P < 0.001). With no differences at baseline, by grade 6, the intervention had lowered IR by 14% (95% confidence interval = 1%–31%) in the boys and by 9% (95% confidence interval = 5%–26%) in the girls, and the percentage of children with IR greater than 3, a cutoff point for metabolic risk, was lower in the intervention than the control group (combined, 22% vs 31%, P = 0.03; boys, 12% vs 21%, P = 0.06; girls, 32% vs 40%, P = 0.05). Conclusions Specialist-taught primary school PE improved IR in community-based children, thereby offering a primordial preventative strategy that could be coordinated widely although a school-based approach.