Birth by caesarean section has been recently implicated in the aetiology of childhood obesity, but studies examining the association have varied with regard to their settings, designs, and adjustment for potential confounders. We conducted a systematic review and meta-analysis to summarize the available evidence and to explore study characteristics as sources of heterogeneity. A search of Medline, EMBASE, and Web of Science identified 28 studies. Random effects meta-analysis was used to calculate pooled risk ratios (RR) with 95% confidence intervals (CI). Caesarean section had a RR of 1.34 (CI 1.18–1.51) for obesity in the child compared with vaginal birth. The RR was lower for studies that adjusted for maternal pre-pregnancy weight than for studies that did not (1.29, CI 1.16–1.44 vs. 1.55, CI 1.11–2.17). Studies that examined multiple early life factors reported lower RRs than studies that specifically examined caesarean section (1.39, CI 1.23–1.57 vs. 1.23, CI 0.97–1.56). Effect estimates did not vary by child's age at obesity assessment, study design or country income. Children born by caesarean section are at higher risk of developing obesity in childhood. Findings are limited by a moderate heterogeneity among studies and the potential for residual confounding and publication bias.