The 21st century is not only the knowledge-based society but also the unifie era for Korea. It implies that Korea should prepare for the unification, especially in the area of knowledge, science, and technology. Under this background, this paper deals with how we can prepare for the unification of South and North Korea in science and technology (S&T) area. There have been no sufficient theoretical studies in this area. This paper, therefore, argues that regional innovation system, which has been developed since the beginning of the 1990s, could be effectively applied to the S&T cooperation and unification between both Koreas. It argues that regional innovation systems can formulate sectoral innovation systems effectively, which lead to a competent national innovation system. According to this study, South and North Korean regions have complementary sectoral innovation systems that could effectively cooperate with each other. Such S&T cooperation could make a great contribution to the S&T integration between two Koreas in the future. This paper argues, therefore, that S&T cooperation between two Koreas should target the unification of South and North Korean regional innovation systems. This paper names it as the unified national innovation system.