Despite several dimensions of area socioeconomic status (SES), past literature has been dominated by the use of area socioeconomic position. We examined the longitudinal effect of three area SES measures (i.e., socioeconomic position, inequality, and segregation) on obesity. Using longitudinal data from the Fragile Families & Child Wellbeing Study (N = 1493), we estimated a linear mixed model to examine the effect of three time-varying area SES measures on time-varying measures of objectively measured body mass index z-score (BMIz) from ages 5 years to 15 years. Findings showed that BMIz increased steadily over time (B = 0.02, 95% CI = 0.02, 0.03). A significant interaction between time and area socioeconomic position indicates that children in areas with higher socioeconomic position had a smaller increase in BMIz than those in low socioeconomic areas (B = − 0.02, 95% CI = − 0.02, − 0.01). A non-linear relationship of area income inequality with BMIz such that BMIz was higher as area income inequality was greater, but the effect diminishes in magnitude with a higher level of area income inequality (linear term: B = 0.07; quadratic term: B = − 0.03). Area income segregation was associated with greater BMIz (B = 0.08, 95% CI = 0.03, 0.12). No time interaction effect was found for area income inequality and segregation. Results highlight a need for community health policy efforts and evidence-based interventions to address childhood obesity issues in low-SES areas.