Early childhood is important for neurodevelopment, and exposure to endocrine disruptors such as bisphenol A (BPA) and phthalates in this period may cause neurodevelopmental disorders and delays. The present study examined the association between exposure to mixtures of BPA and three metabolites of phthalates in early childhood and IQ at 5 years of age. The Mother and Children's Environmental Health (MOCEH) study is a prospective birth cohort study conducted in Korea with 1751 pregnant women enrolled from 2006 to 2010. After excluding those without relevant data, 47 children were included in the final analysis. We measured children's urinary concentrations of metabolites of endocrine-disrupting chemicals (Bisphenol A, mono-(2-ethyl-5-oxohexyl) phthalate, mono-(2-ethyl-5-hydroxyhexyl) phthalate and mono-(2-ethyl-5-butyl) phthalate) at ages of 24 and 36 months. We evaluated the children's IQ with the Korean Wechsler Intelligence Test at the age of 5 years. After adjusting for potential confounders, a multiple linear regression was conducted to examine the associations between individual endocrine-disrupting chemicals and the IQ of the children. Weighted Quantile Sum (WQS) regression and quantile-based g-computation were used to assess the association between IQ at age 5 and exposure to mixtures of BPA and phthalates. In the single-chemical analyses, mono-(2-ethyl-5-butyl) phthalate exposure at 36 months was adversely associated with children's IQ (β = −4.93, 95% confidence interval (CI): -9.22, −0.64). In the WQS regression and quantile-based g-computation analyses, exposure to the mixture of BPA and phthalates was associated with lower IQ [β = −9.13 (P-value = 0.05) and β = −9.18 (P-value = 0.05), respectively]. The largest contributor to the overall association was exposure to mono-(2-ethyl-5-butyl) phthalate at 36 months. In the present study, postnatal exposure to mixtures of BPA and three metabolites of phthalates was associated with decreased IQ of children at age 5.