For years, body mass index (BMI) has been used by scientists to track weight problems and obesity in children and adults. Recent studies have implicated the fat mass and obesity gene (FTO) in the increase of BMI in young adults. A longer duration of breastfeeding is known to reduce the risk of being overweight later in life, but its ability to modify the effect because of FTO is not known.Methods We studied 1096 children from the Western Australian Pregnancy (Raine) cohort who were followed up from birth to 14 years of age. Linear mixed-effects models were used to investigate BMI growth trajectories in boys and girls separately.Results An association was found between BMI growth and the duration of exclusive breastfeeding (EXBF) among carriers of the risk allele of the FTO SNP rs9939609. In girls, EXBF interacts with the SNP at baseline and can reverse the increase in BMI because of SNP risk allele by age 14 years after 3 months of EXBF. In boys, EXBF reduces BMI both in carriers and non-carriers of the risk allele with an association found after 10 years of age. Six months of EXBF will put the boys’ BMI growth curves back to the normal range.Conclusions Our study could have major health implications by providing new perspectives for the prevention of growth problems in children carrying risk alleles in the FTO gene.