The purpose of this study is to analyze the efficiencies of project management offices in large information system construction projects using the data envelopment analysis. In addition, we tried to estimate the confidence interval of those efficiencies using bootstrap DEA to give a statistical meaning. The efficiency by the CCR model is analyzed as eight project management offices are fully efficient and 22 project management offices are inefficient. On the other hand, there are 15 project management offices are fully efficient, but 15 project management offices are inefficient in the BCC model. As the result of the scale efficiencies, of the inefficient project management offices, 13 project management offices are inefficient in scale. It is possible to eliminate the inefficiency in the CCR model by improving their project performances. And, the nine project management offices showed that the inefficiency was due to pure technical efficiency, and these companies should look for various improvements such as improvement of project execution system and project management process. In order that the inefficient project management offices be efficient, it is analyzed that more efforts must be made for on-budget and on-time as a result of examining the potential improvement potentials of inefficient project management offices.