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This paper presents a framework to analyze the change in the research and development (R&D) efficiency of government-funded research institutes (GRIs) in Korea. Cumulative data envelopment analysis/Malmquist index method is utilized to analyze the changes in R&D efficiency of GRIs. Data analysis of the R&D activities of 10 GRIs in Korea Research Council of Fundamental Science & Technology showed that the average R&D efficiency of the 10 GRIs improved from 2009 to 2013. However, the efficiency of a few GRIs decreased in terms of the catch-up index. The proposed framework can help management teams diagnose the current state of R&D activities and determine the efficacy of strategic actions by comparing efficiencies in the past.