This paper tries to observe the cost structure in two prominent Islamic banks in Indonesia. The Bank’s cost structures are viewed in many ways such as operational and non-operational costs, and fund costs and non-fund costs.The study employed descriptive analysis to explain the data characteristics from the banks and tried to make evaluation by comparing the data within the same time. The result of the study showed that there was a similarity about those Islamic bank’s cost structures behavior, but there were also some differences among those within the study period. By using inferential statistics method, especially with mean-differences test, the study demonstrated that the null-hypothesis was rejected which means that there were differences about the cost structures between both Islamic banks within the period.