Childhood obesity affects both pubertal growth and pubertal timing. We evaluated pubertal timing-mediated effects of childhood obesity on pubertal growth. This retrospective, representative-population-based cohort study included 6,733 boys and 6,916 girls born between April 1975 and March 1976 in Akita Prefecture, Japan. Individual changes in height standard deviation score between 7 and 17 years (ΔHtSDS), body mass index Z-score at 7 years (BMIZ), and estimated age at peak height velocity (ÂPHV) were used as surrogate indicators of pubertal growth, childhood obesity and pubertal timing, respectively. ÂPHV-mediated effect of BMIZ on ΔHtSDS was evaluated, and non-ÂPHV-mediated effect was calculated. Based on BMIZ, participants were categorized into three groups (underweight, normal-weight and obese groups), and the differences in ΔHtSDS between obese and normal-weight or underweight groups and ratios of non-ÂPHV-mediated effect were determined. ΔHtSDS values in the obese group were lower by 1.23 in boys and 1.17 in girls than those in the underweight group and by 0.87 in boys and 0.85 in girls than those in the normal-weight group. Non-ÂPHV-mediated effect on the reduced ΔHtSDS in the obese group compared to the underweight and normal-weight groups accounted for 68% and 71% in boys and 59% and 64% in girls, respectively. Thus, childhood obesity is associated with reduced pubertal growth regardless of pubertal timing. This reduced pubertal growth observed in children with obesity could be more affected by non-pubertal timing-mediated effect rather than pubertal timing-mediated effect.