Abstract Background Accumulating evidence suggests that phthalate exposure affects neurodevelopment, including emotional and behavioral outcomes. Our aim was to investigate if prenatal phthalate exposure affects the developmental course of internalizing and externalizing symptoms from early childhood to adolescence. Methods Concentrations of seven phthalate metabolites were measured in first-trimester maternal spot urine samples, and DEHP, and high and low molecular weight phthalate concentrations were calculated (HMW and LMW, respectively). Mothers reported internalizing and externalizing symptoms via the Strengths and Difficulties Questionnaire at 4 years and the Child Behavior Checklist at 6, 11 and 15 years. Group-Based Trajectory Modeling was used to classify 546 participants of the Rhea Cohort (Crete, Greece) into 4 distinct groups (Stable low, Stable high, Low-Increasing, and High-Decreasing symptoms). We evaluated the association of prenatal phthalate exposure with the odds of an adverse (Stable high, Low-Increasing, and High-Decreasing) internalizing and externalizing symptom trajectory in 150 children using multivariable-adjusted logistic regression (reference group: stable low). Results Only for girls, exposure to DEHP and HMW phthalates was associated with higher odds of being grouped in an adverse internalizing symptoms trajectory (OR [95%CI]: 1.52 [1.03, 2.25] and 1.57 [1.03, 2.39], respectively). Regarding externalizing symptoms, interactions with gender emerged for DEHP (p = 0.024) and HMW (p = 0.028) phthalates, and increased odds of being grouped into an adverse trajectory were observed in girls, whereas boys showed the opposite trend, albeit none reached statistical significance. Conclusions The findings suggest programming effects of prenatal phthalate exposure on the developmental course of emotional symptoms in girls. Further research is needed to clarify the association between in utero phthalate exposure and behavioral symptoms. Key messages • Phthalate exposure is linked to adverse trajectories of emotional symptoms, emerging from preschool age and up to adolescence. • Phthalate effect on internalizing and externalizing symptoms varies by gender.