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Abstract Introduction In Japan, there are approximately 300 projects conducting research on rare diseases supported by the Ministry of Health, Labour and Welfare of Japan (MHLW) and the Japan Agency for Medical Research and Development (AMED). Diverse data, including clinical, genomic, and sample‐related data, are generated by these projects. However, at present, such data are managed individually by each project. This makes it difficult for third parties to ascertain the data generated by projects. Methods Again this background, at the beginning of 2017, the AMED started the National Platform for Rare Diseases Data Registry of Japan (RADDAR‐J), whose mission is to construct a cross‐sectional data integration platform incorporating projects supported by the AMED and MHLW. RADDAR‐J promotes data sharing by the projects in accordance with the data‐sharing policy established by the AMED, which classifies data sharing into three categories based on the strategies used to protect the rights of researchers while promoting data sharing. RADDAR‐J integrates and analyzes data shared by each project to add value to the resources and promote secondary use by third parties while protecting the rights of the researchers who shared their data. The platform is designed to provide incentives to projects that shared their data by supporting registry construction or genomic analysis to promote data sharing. RADDAR‐J also has the function of data identification to securely integrate data originating from the same person. RADDAR‐J accelerates clinical research by encouraging each project to utilize a central ethics committee. Results/Conclusion The use of the platform by projects is expected to lead to streamlined data collection, improved quality assurance, improved access to data, and promotion of joint research and the secondary use of shared data. These benefits will accelerate research into diagnosis and treatment technologies and will hopefully lead to improved quality of life for patients with rare diseases.