This study shows the scientific and systematic Evaluation Model using factor analysis and AHP methods for the success of defense Information System R&D projects. The evaluation model was divided into 7 evaluation factors such as Developing support, Developing infrastructure, Developing management and test & evaluation, Support factors for strength, Understanding & developing strategy, Developing technology & organization, and Developing performance. And those were composed of totally 24 low level Evaluation index. The Developed Evaluation Model in the paper could be contributed more to objectively and transparently company selection of defense Information System R&D and other defense R&D Projects in the future.