Korea’s R&D intensity was 4.64% in 2019, the second-highest among OECD member countries after Israel (4.90%). R&D investment can enhance the productivity of firms by promoting technological progress and innovation. In Korea, R&D investment has continuously increased, but there are various opinions on the effectiveness of R&D investment because the productivity of R&D investment differs on how R&D productivity is defined and the measurement index used. In addition, literature related to productivity changes and R&D investment effects at the firm level is sparse. Therefore, in this study, R&D productivity was estimated using stochastic frontier analysis and the Malmquist productivity index based on firms participating in the Korean emissions trading scheme (KETS). From the empirical results, it is concluded that R&D productivity has been steadily declining compared to previous years. The factor most strongly influencing fluctuations in R&D productivity is efficiency change. In addition, estimated total factor R&D productivity is increasing and the increased value is statistically significant after the introduction of the KETS. On comparative analysis across industries, industries with the highest total factor R&D productivity among the 12 industries were petrochemical, machinery, and semiconductor industries. Textile, power generation/energy, and non-ferrous metal industries had low R&D productivity.