In recent years, researchers have focused on the problems of Japanese regional disparity. The fiscal transfer system plays an important role in the decentralization of power; thus, this paper examines the impact of fiscal transfers on regional disparity. Specifically, we collected data on regional government revenue from different prefectures between 1989 and 2015. The coefficient of variation of per capita revenue each year was calculated using different types of fiscal transfers. The coefficient of variation was then used to analyze the impact of fiscal transfers on regional disparity. Different types of fiscal transfers have different effects on regional disparity. For example, local allocation tax has expanded regional disparity and these effects were analyzed separately. In addition, the influence of financial dependence on regional disparity was also analyzed. The results of these analyses show that fiscal transfers expand the regional disparity of different prefectures, with differing influences that different methods of fiscal transfers have on regional disparity. A negative correlation was also observed between the regional disparity gap and the coefficient of variation of financial dependence. Finally, measures are proposed to improve the current situation of regional disparity.