The study investigates Taiwan's sectoral system of innovation in the pharmaceutical industry, which has failed to achieve international competitiveness, despite strong state support. Our investigations were designed and carried out in two stages. In the first stage, we developed a statistical method to measure the institutional drivers in Taiwan's pharmaceutical industry. This finding received strong support in our second stage of analysis, which involved the use of both: (1) inductive processes (through the use of interviews) and (2) deductive (i.e., mathematical) approaches to analyze the innovation performance in Taiwan's pharmaceutical industry. In particular, we compared patenting and publication activities in Taiwan versus those of India. The results of our study demonstrate that the intellectual property regime (i.e., patents and publications) is playing a critical role in linking actors and institutions and is highly associated with the effectiveness of the innovation system in the pharmaceutical sector.