This study suggests the applicability of an AHP(Analytic Hierarchy Process) to improve the validity and fairness of evaluation index to assess the defense core-technology R&D projects. This study focused on the design of the proposal and performance evaluation index to structure them into a hierarchy using AHP which can be applicable to take the opinion of the defense R&D experts. Using the refined evaluation index, we propose a technique to enhance the reliability of the defense R&D projects evaluation system.