Under circumstances with increasing uncertainty, strategic flexibility has become an essential point on which my R&D management system should be based. Unfortunately the present R&D management system for government sponsored R&D programs cannot be said to be so flexible to adapt appropriately to various threatens such as technological failure, a severe change in competition environment, and so on. In this paper a new scheme for R&D planning and economic assessment with strategic flexibility is suggested and applied to a real R&D program. In the newly suggested R&D management system, economic valuation based on real option theory is performed for various alternative scenarios which have different strategic scheme for R&D process each and the result of the assessment is fed back to R&D planning to choose more superior strategic scheme. Introducing strategic flexibility into R&D planning and economic assessment, the value of R&D project could be remarkably enhanced.