The purpose of this study is to investigate the relationship between R&D investment and firm performance in the Korean stock market and to investigate the moderating effect of R&D expenditure increase. The empirical analysis period covered in this study is 12 years from 2001 to 2012, and the total number of sampled firms is 6,216. The sample covered in this study is extracted from all listed companies on the Korea Exchange except for the financial industry. The conclusions obtained from this study are summarized as follows from the empirical analysis results. First, The reason that the R&D investment results in a decrease in the accounting profit is that the R&D expenditure is amortized or is treated as cost in accounting. On the other hand, R&D investment is considered to lead to an increase in market performance because if the firm increases investment in research funds, it will be responded with good results in the market. Second, although the increase in R&D investment does not affect the accounting performance, there is a moderating effect on the market performance in which R&D investment increases the market performance. However, there is no statistical significance for the accounting performance, but the sign of the regression coefficient is negative, so that the increase of R&D expenditure further decreases the accounting performance. Third, in this study, the adjustment effect of R&D investment is analyzed by dividing total sample into sub-samples such as large enterprises, SMEs, KOSPI firms, and KOSDAQ firms. As a result, the regression results show statistically significant results only for large firms and KOSPI firms. This result can be interpreted that large companies and KOSPI firms have a smaller investment value than SMEs and KOSDAQ companies, but the market evaluation of investment increase is high. Fourth, for the sub-sample composed of large corporations and KOSPI firms, R&D investment moderating effect also appears on the return on asset, accounting performance. This result shows that the moderating effect model of R&D investment is also applied to accounting performance. The results of this study suggest that CEOs have positive implications on R&D investment and the moderating effect of R&D investment. In addition, the moderating effects presented in this study are first presented in this field of study. Also, this study suggests that the CEO’s decision-making guide to R&D investment affects all market performance and that continuous investment increase leads to improvement of market performance.