Objective The epidemiologic link between cesarean birth and childhood obesity is unresolved, partly because most studies come from industrialized settings where many post‐birth factors affect the risk for obesity. We take advantage of an unusual ethnographic situation where hospital and cesarean birth modes have recently been introduced among Yucatec Maya subsistence farmers, but young children have had minimal exposure to the nutritional transition. While we expect to find very low rates of childhood obesity, we predict that cesarean‐born children will be larger and heavier than vaginally born children. Methods Weight and height were collected monthly on 108 children aged 0–5 (3576 observations total). Birth mode and birthweight were collected by maternal interview. Data were analyzed using linear mixed models that compare child growth [Maya population‐specific Z‐scores for weight‐for‐age and body mass index‐for‐age (WAZ and BMIZ)] in cesarean and vaginally born children aged 0–5 years. Results The cesarean rate was 20%, no children were obese, and 5% were overweight. Cesarean birth was a significant predictor of child WAZ and BMIZ after accounting for maternal effects, child birthweight, and sex. Children who were born by cesarean to mothers with high BMI had the highest WAZ of all children by 5 years of age, and the highest BMIZ of all children at all ages. Conclusion Cesarean‐born Maya children had higher BMI than vaginally born children, even in the absence of many known confounding factors that contribute to childhood obesity. Child growth was most sensitive to birth mode when mothers had high BMI.