This paper presents a systematic approach for evaluating the performance of a project based organization using a two level fuzzy data envelopment analysis (DEA) technique in project based organizations. In order to determine the required inputs and outputs, important indicators are selected using both expert judgments and statistical analysis and a two-level DEA model is adapted. In this model, by considering different inputs and outputs through a hierarchical process, a large number of sub indicators are provided and rolled up to a higher level. Since inputs and outputs are combinations of qualitative and quantitative indicators, fuzzy logic is also included through the modeling procedure. In addition, since the exact amount cannot be attributed to the indicators, the proposed model uses interval values for the project life cycle. Finally, some of the projects are evaluated throughout the approach proposed in this paper.