Japan is one of the largest pharmaceutical markets in the world, and as such, pharmaceutical companies are intensively conducting research and development of new drugs in Japan. However, information on Japanese pharmaceutical market profiles is limited. In this context, we elucidated the market characteristics and trends of new molecular entities approved between 2006 and 2015 in Japan. Among antineoplastic and immunomodulating agents, the highest number was first approved in the United States, and for nervous system drugs, the highest number was first approved in Europe. The alimentary tract and metabolism and the musculoskeletal system were the therapeutic areas for which the most drugs were approved for the first time in Japan. Most of the musculoskeletal system drugs were developed by Japanese companies, and most of the antineoplastic and immunomodulating agents were developed outside of Japan. Using various performance indexes, such as market forecasts and significance of clinical benefits, we determined that the number of new molecular entities and market size increased and the number of drugs with significant clinical benefits decreased. These results suggest that new molecular entity innovation by Japanese companies has been decreasing and the government’s comparative method for pricing does not work well in Japan.