Abstract: With Japan as the target for reference and on the basis of systematic analysis of orphan drug regime in Japan, this paper analyzed orphan drug regime in Japan from the aspects of pre-approval designation, approving and marketing phase and post-marketing administration, and also provided the corresponding operating performance evaluation. The study results indicated that the mature orphan drug system in Japan has yielded good effects in that it has effectively facilitated orphan drug R&D and improved the access, thereby providing referable and valuable theoretical foundation for the construction of orphan drug regime in China.