Due to increasingly strained governmental resources, effective management and efficient utilization of government funds for R&D projects has become a critical issue. This study aimed to design performance indices and the associated mechanism to assist the National Science Council (NSC) of Taiwan in evaluating the performance of government funded R&D projects to enhance the decision quality for government R&D funding. In particular, a hierarchy of performance indices was developed that can be employed for different types of R&D projects with the corresponding weighting. Then, a novel mechanism with systematic procedures was designed to undertake the evaluation before, during, and after the project execution for feed forward and feedback control of government funded R&D projects. Therefore, the collected performance data can be analyzed for effective project management and rational resource allocation decisions. This study concludes with discussions of future studies.