Background The built environment is an important contributor to childhood obesity; however, large-scale and longitudinal studies designed to examine their associations remain limited. This study aimed to examine whether walkable neighborhoods were associated with childhood obesity risk over a 9-year period. Methods We used data collected in the US nationally representative Early Childhood Longitudinal Study – Kindergarten (ECLS-K) Cohort, with 9440 kindergarteners followed up until their 8th grade (1998–2007). Four built environmental variables, street intersection density, residential density, fitness facility density, and recreational facility density, were calculated from national census, business, and road network datasets, and then matched with ECLS-K samples. Mixed-effect models were performed to estimate associations between built environments and child weight status. Results Children who experienced increased intersection density during 1998–2007 had a lower BMI in 2007 (β = −0.49, p < 0.01), especially girls (β = −0.79, p < 0.01) and suburban children (β = −0.66, p < 0.05). They also had lower obesity risk in 2007 (OR = 0.79 [95% CI = 0.66–0.94]), especially girls (OR = 0.68 [95% CI = 0.52–0.88]). Girls and boys who lived in neighborhoods with the higher (but not highest) residential density in 1998 showed lower obesity risk (OR = 0.54 [95% CI = 0.30–0.98]) and overweight risk (OR = 0.54 [95% CI = 0.30–0.95]) in 2007, respectively. Conclusions National data indicate that in the US greater walkability in residential neighborhoods may lead to lower child BMI and obesity risk after nine years, and the association was stronger among girls and in suburban regions. This provides useful evidence for future obesity prevention and urban planning.