The relationship between early childhood phthalate exposure and early adiposity rebound (EAR) is unclear. This study aimed to investigate the association between 1.5- and 3-year phthalate exposure and EAR and overweight/obesity in 7.5-year-old Japanese children. A total of 452 mother–child pairs were enrolled from the Aichi Regional Cohort of the Japan Environment and Children's Study. The children were followed up at birth and at 1.5, 2, 3, 4, 5, 6, and 7.5 years of age for physical examination. Human biomonitoring of 16 urinary metabolites of eight phthalates was performed at 1.5 and 3 years of age. Latent class mixed models, binary logistic regression, and quantile g-computation were performed to identify body mass index (BMI) trajectories and investigate the relationships of single or mixed phthalate exposure with EAR and overweight/obesity. A one-unit increase in log10-transformed 3-year-old Σdi(2-ethylhexyl) phthalate (ΣDEHP) exposure levels was significantly associated with 6-year-old BMI in girls. The 1.5-year mono-iso-butyl phthalate and 3-year Σdi-isodecyl phthalate exposure levels were significantly associated with the repeated measures of longitudinal BMIs in girls. Single phthalate exposure showed null associations with EAR or overweight/obesity in the 7.5-year-old children. Σdi-isononyl phthalate, ΣDEHP, and mono-n-butyl phthalate exhibited the highest proportion of partial positive weights of being in the EAR trajectory after confounder adjustment. Phthalate mixture exposure in 1.5- and 3-year-old children was not significantly associated with EAR. Early childhood phthalate exposure was not related to EAR or overweight/obesity in 7.5-year-old Japanese children. However, few phthalates were positively associated with longitudinal BMIs in girls.