Cesarean birth leads to a markedly different microbiome compared to vaginal birth, and the microbiome has been implicated in childhood obesity. Among mothers who had a previous cesarean, we compared anthropometry of 3- to 6-year-old children who were subsequently born by cesarean section versus vaginal birth. This large population-based study involved linking de-identified administrative perinatal and anthropometric data. Children's weight and height were collected at community-based clinics and converted to age- and sex-adjusted z-scores of height-for-age (HFAz), weight-for-age (WFAz) and BMI-for-age (BMIz). The average treatment effect (ATE) of cesarean versus vaginal birth was calculated from augmented inverse probability weighted analyses accounting for a wide range of confounding variables. There was little evidence of an effect of cesarean birth on HFAz (ATE = 0.26 95%CI −0.35, 0.87, n = 3993), WFAz (ATE = 0.35, 95%CI −0.19, 0.89, n = 4817) or BMIz (ATE = 0.11, 95%CI −0.25, 0.46, n = 3909). Cesarean section was not associated with anthropometry among children aged 3–6 years.