Background: A high prevalence of prenatal alcohol exposure has been reported among children in care and thus, the risk of fetal alcohol spectrum disorder (FASD) in this population is high. Objective: The purpose of the current study was to estimate the number of children (0-18 years) in care with FASD and to determine the associated cost by age group, gender, and province/territory in Canada in 2011. Methods: The prevalence of children in care by province/territory was obtained from the Canadian Child Welfare Research Portal, and the number of children in care with FASD for each province/territory was estimated from available epidemiological studies. In order to calculate the total cost per province/territory, the cost per individual per day, by age group, was applied to the respective number of children in care with FASD. Results: The estimated number of children in care with FASD ranged from 2,225 to 7,620, with an annual cost of care ranging from $57.9 to $198.3 million Canadian dollars (CND). The highest overall cost ($29.5 to $101.1 million CND) was for 11-15 year-olds. Conclusion: The study findings can be used to demonstrate the substantial economic burden that FASD places on the child welfare system. Attention towards the needs of this population and prevention efforts to reduce FASD incidence in Canada, and other countries are urgently needed.