Background: As abundant evidence shows the composition of gut flora in children born by caesarean section is different from that of vaginal delivery children, studies on whether caesarean section would increase the offspring's risk of developing allergic disease attract extensive attention. However, the results of different researches are inconsistent. Therefore we conduct a systematic review and meta-analysis to explore the relationship between caesarean section and childhood allergic disease. Methods: The protocol followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols. Cohort studies for investigating the relationship between caesarean section and the risk of childhood allergic disease will be searched in 4 main databases (PubMed, EMBASE, the Cochrane Library, and the web of science). In addition, a manual search of the references of relevant published studies will also be considered. Four common allergic outcomes will be included: asthma, allergic rhinitis, food allergy, and atopic dermatitis. Studies selection, data extraction, and risk of bias assessment will be conducted by 2 independent reviewers. The primary outcome is the incidence of 4 allergic diseases. Results: The results will provide useful information on whether caesarean section contributes to the increase of allergic disease in children. Conclusion: The findings of this study will be published in a peer-reviewed journal. PROSPERO registration number: CRD42019135196.