Background Cesarean Section (CS) delivery has been increasing rapidly worldwide and Bangladesh is no exception. In Bangladesh, the CS rate has increased from about 3% in 2000 to about 24% in 2014. This study examines trend in CS in Bangladesh over the last fifteen years and implications of this increasing CS rates on health care expenditures. Methods Birth data from Bangladesh Demographic and Health Survey (BDHS) for the years 2000–2014 have been used for the trend analysis and 2010 Bangladesh Maternal Mortality Survey (BMMS) data were used for estimating health care expenditure associated with CS. Results Although the share of institutional deliveries increased four times over the years 2000 to 2014, the CS deliveries increased eightfold. In 2000, only 33% of institutional deliveries were conducted through CS and the rate increased to 63% in 2014. Average medical care expenditure for a CS delivery in Bangladesh was about BDT 22,085 (USD 276) in 2010 while the cost of a normal delivery was BDT 3,565 (USD 45). Health care expenditure due to CS deliveries accounted for about 66.5% of total expenditure on all deliveries in Bangladesh in 2010. About 10.3% of Total Health Expenditure (THE) in 2010 was due to delivery costs, while CS costs contribute to 6.9% of THE and rapid increase in CS deliveries will mean that delivering babies will represent even a higher proportion of THE in the future despite declining crude birth rate. Conclusion High CS delivery rate and the negative health outcomes associated with the procedure on mothers and child births incur huge economic burden on the families. This is creating inappropriate allocation of scarce resources in the poor economy like Bangladesh. Therefore it is important to control this unnecessary CS practices by the health providers by introducing litigation and special guidelines in the health policy.