We investigated the effect of snacking habits in childhood on changes in body mass index (BMI) and high BMI in adolescence and adulthood. In total, 2141 Japanese children from the Ibaraki Children's Cohort Study were evaluated at age 6 years (baseline), then at ages 12 and 22 years. We examined associations between snacking (scheduled times, when children wanted, and freely) at age 6 years and changes in BMI over time and the proportion of high BMI at ages 12 and 22 years, using time-dependent mixed-effects and logistic regression models. Compared with children who snacked at scheduled times, those provided snacks when they wanted experienced larger increases in BMI over time between ages 6 and 22 years (multivariable time-dependent effect: 0.03 kg/m2 for boys, p = 0.047; 0.04 kg/m2 for girls, p = 0.019). No differences were observed in children who snacked freely. A higher proportion of high BMI was found in boys who were provided snacks when they wanted compared with those who snacked at scheduled times. The multivariable odds ratio (95% confidence interval) was 1.52 (1.04-2.23) at age 12 years and 2.23 (1.12-4.45) at age 22 years. No differences were observed for girls at either age. Children who were provided snacks when they wanted showed larger increases in BMI over time compared with those who snacked at scheduled times. Boys who were provided snacks when they wanted showed the higher proportion of high BMI at follow-up.