This research aims to explore the mode of River Basin Management (RBM) in Korea and Japan with a comparative perspective. The efforts of implementation of RBM in Korea have included the several attempts to enact the Basic Water Bill, and river basin environmental offices and committees in the four major rivers. Japan has also endeavored to introduce policy efforts to accommodate the new approach including the establishment of river basin comprehensive water resources management committees. Despite such policy efforts, the comparative analyses indicate a series of challenges. The first challenge is to transfer the relevant power from center to river basins. Second, there is a lack of laws and regulations to support a set-up of RBM. Third, river basin organizations are not compatible with the current administrative systems in Korea and Japan. Fourth, river basin organizations require independent funding. Fifth, there are conflicts between ministries involved in water management. It is concluded that more emphasis should be placed on establishment of adequate institutions and legal settings in order to establish RBM in these countries alongside political commitment.