The Korean government has invested in national R&D programs since the early 1980s, and evaluation activities ensued. This paper is written (1) to explain the experience of evaluating projects of the national R&D programs, (2) to investigate the specific problems related to the present evaluation system, and (3) to recommend guidelines for future improvement in the evaluation practice. The Korean experience should be of some reference value to other countries in designing or implementing national R&D project evaluation systems.