Background Perfluorooctanoic acid (PFOA) is widely used in daily life, however, research has shown its immune suppression function. Our aim is to investigate the relationship between prenatal exposure to PFOA and allergic diseases in children. Methods A prospective birth cohort study involving 648 pregnant women was conducted. Prenatal information was collected by an interview with the women and from medical records. Fetal umbilical cord blood was collected, and concentration of PFOA and genotype of IL-13 rs20541 were detected. Children were followed at 6, 12 and 24 months and information on the development of allergic diseases was recorded. Multivariate logistic regression analysis was used to examine the association between PFOA and allergic diseases. Stratified analysis was performed based on gender and genotype of IL-13 rs20541. Results In multivariate adjusted models, the highest PFOA quartile is associated with odds of atopic dermatitis (AD) (OR 1.66, 95% CI 1.09-2.55), wheezing (OR 4.06, 95% CI 1.30-12.68), and allergic diseases (OR 1.71, 95% CI 1.15-2.54). Female patients with the highest PFOA quartile have a higher odd of AD (OR 2.25, 95% CI 1.20-4.23) and allergic diseases (OR 1.93, 95% CI 1.07-3.46). Patients with GG genotype of IL-13 rs20541 and the highest PFOA quartile also have a higher odd of AD (OR 2.82, 95% CI 1.41-5.67), wheezing (OR 15.16, 95% CI 1.38-166.59), and allergic diseases (OR 2.42, 95% CI 1.27-4.61). Conclusions Prenatal exposure to PFOA increases the risk of developing allergic diseases in children, especially for the female patients and those with the genotype of IL-13 rs20541 GG.