<p>This study evaluates how interregional accessibility affects the efficiency of Japan’s regional innovation system (RIS), focusing on patent intensity efficiency. In previous studies, little is known about how the conditions under which borrowed size, facilitated by high-quality high-speed rail systems, promotes innovation activities can be used to improve the functionality of RIS. Therefore, this study evaluates the determinants of RIS efficiency based on a stochastic frontier analysis using patent data. The results showed that employment density and establishment size significantly affect patent intensity, confirming the impact of agglomeration economies. In particular, regional innovation activities are centered on large-scale establishments, and the results suggest the importance of ample research and development investment. Furthermore, the borrowed size effect was revealed as a significant factor in determining the efficiency of RIS, and that accessibility to large metropolitan areas was shown to enhance regional innovation capacity. Conversely, the installation of high-speed transportation systems, such as the Chuo Shinkansen (Maglev), may increase economic disparities between large metropolitan areas and geographically isolated rural areas.</p>