In this study, we develop an approach based on analytic network process (ANP) and data envelopment analysis (DEA) to evaluate the performance of Research and Development projects. We identify a set of criteria and subcriteria having interdependencies among themselves. Interdependency is treated using a hybrid ANP model consisting of both hierarchy and network. The interval pairwise comparison matrices are constructed in a group decision-making process. ANP is extended to obtain interval weights from the interval pairwise comparison matrices. Interval weights are formulated as assurance region constraints in a super-efficiency DEA model, through which the project ranking is obtained. The super-efficiency DEA model is also modified to handle missing data. The approach is applied to a real case study on performance evaluation of the ongoing projects in a Defense Research and Development Institute.