Cost Estimating allows each entity in a construction project to plan, distribute, and control its required construction cost for the project. However, existing 2D design based estimating has problems, such as inaccuracy and inefficiency caused by missing, duplicated, or erroneous calculations. In this situation, current estimations for school facilities have more difficulties in forecasting construction costs due to an inadequate work breakdown structure for BOQ (Bill of Quantity) and insufficient guidelines for Basis of Estimate. In this study, therefore, an effort was made to increase the efficiency of estimating for school facilities by applying a 3D modeling based BIM tool to quantity and cost estimates. In addition, this study suggested a reasonable work breakdown structure for BOQ that was appropriate when 3D modeling was applied, and verified it through a case study. The authors tried to provide a BIM-based estimating method for school facilities to obtain greater accuracy and efficiency by having more information in an earlier stage.