Prenatal exposure to phthalates might influence the development of childhood obesity. Most previous studies used body mass index (BMI) at a specific age instead of BMI development, which might be a better indicator of later health. We aimed to assess the association of prenatal phthalate exposure with longitudinal BMI development from infancy to adolescence. Among 1,379 mother-child pairs from a population-based cohort study, phthalate concentrations were measured in maternal spot urine samples, collected during first, second and third trimester. We estimated age- and sex-adjusted BMI standard deviation scores (SDS) at 6 months and 1, 2, 3, 4, 6, 10 and 13 years. We examined the associations of maternal phthalate urine concentrations during pregnancy with repeated measures of BMI using linear mixed effects models. An interquartile range higher natural log-transformed maternal first trimester high-molecular weight phthalate and di-2-ethylhexylphthalate (DEHP) urine concentrations were associated with a -0.10 (95% confidence interval (CI) -0.15 to -0.04), and -0.09 (95% CI -0.15 to -0.04) lower age- and sex-adjusted BMI at 6 months. An interquartile range higher natural log-transformed maternal first trimester phthalic acid and low-molecular weight phthalate urine concentrations were associated with a 0.11 (95% CI 0.03 to 0.18) and 0.13 (95% CI 0.04 to 0.21) higher age- and sex-adjusted BMI at 13 years old. No significant associations were observed for maternal second and third trimester phthalate urine concentrations with BMI. Thus, higher maternal phthalate metabolites urine concentrations appear to be related to lower BMI at early ages but with higher BMI at later ages.