The recent exponential increase in caesarean section (CS) rates in many countries including Ghana requires an understanding of the potential long-term consequences on child health. The present study investigated the relationship between CS delivery and risk of childhood overweight/obesity. A retrospective cohort study was conducted from October 2019 to March 2020 in Ghana. Using multi-stage sampling, 553 mother–child pairs aged 6–23 months were selected from ten health facilities during child welfare clinic (CWC) services. We assessed the association between delivery mode (caesarean v. vaginal) and subsequent body mass index for age (BMI/age Z-score) using hierarchical multivariable linear regression analysis. The prevalence of overweight/obesity (BMI/age Z-score > +2 sd) in children was 3⋅6 %. After adjusting for maternal gestational weight gain, macrosomia and child feeding practices, children who were born through CS had mean BAZ which was 0⋅105 standard units significantly higher than their colleagues who were delivered through normal vaginal [beta coefficient (β) 0⋅105, (95 % CI 0⋅03, 0⋅55)]. CS birth was also associated with 3⋅2 times higher odds of overweight/obesity than vaginal delivery (AOR 3⋅23; 95 % CI 1⋅14, 9⋅13). Consequently, CS delivery was associated positively with increased body mass (adiposity) in the study sample. The association between CS delivery and risk of childhood obesity was attenuated after adjusting for macrosomia. These results would be important for informing clinicians and expectant mothers in considering CS delivery.