Although technological innovation is critical for growth and future survival, small and medium scale enterprises (SMEs) are at a disadvantage compared to larger organizations given the resources available. It is important to examine the possible methods for making research and development more efficient. This study analyzes the technological innovation efficiency of SMEs in the manufacturing and service industries in South Korea and determines the factors affecting efficiency. The models of data envelopment analysis and Tobit regression analysis were used. According to the analysis results, the technical and pure technical efficiencies were higher in the service industry than in the manufacturing industry. The factors affecting efficiency were also different between the two industries. This study is significant because it evaluates the innovation activity efficiency of small and medium manufacturing and service companies in South Korea and provides specific criteria and a rationale to improve the efficiency.