Background: Globally, the incidence of allergic diseases is increasing along with cesarean delivery rates. Data regarding the association between cesarean delivery and allergic diseases are inconsistent. Here, we aimed to clarify the association between cesarean delivery and the development of asthma, atopic dermatitis, wheezing, and eczema. Methods: We used data from the Japan Environment and Children’s Study. The data included were those of 104,065 fetal records and their children. Information about the mode of delivery, asthma, atopic dermatitis, wheezing, and eczema was obtained from questionnaires and medical record transcripts. Multiple logistic regression analysis was used to assess the association between cesarean delivery and asthma, atopic dermatitis, wheezing, and eczema risk among infants at 1 year of age. Results: We included 74,639 subjects in this study, wherein 18.4% underwent cesarean deliveries. After adjusting for the perinatal, socioeconomic, and postnatal confounding factors, children born by cesarean delivery had no increased risk of developing asthma [95% confidence interval (CI) 0.84–1.08], atopic dermatitis (95% CI, 0.92–1.13), wheezing (95% CI, 0.94–1.04), or eczema (95% CI, 0.94–1.05). Conclusions: This nationwide cohort study found no association between cesarean delivery and asthma, atopic dermatitis, wheezing, and eczema among infants at 1 year of age. However, further studies are needed to evaluate whether cesarean delivery plays a role in the development of allergic diseases.