Several classifications have been proposed to define rare cancers; however, the pathophysiological understanding of tumors evolves rapidly. We propose a New Classification of Rare Cancer (NCRC) using the updated International Classification of Diseases for Oncology 3.2 coding system and World Health Organization Classification of Tumors 5th edition. We applied patient data recorded in the National Cancer Registry of Japan to the new classification, setting a cut-off of a crude incidence rate of 6 cases/100 000/year to define rare cancers, and developed a list of rare cancers in Japan from 2016 to 2019. The NCRC system identified various rare cancers, comprising 20.0% of all cancer diagnoses in this period. To examine this classification system's performance, we compared rare/non-rare labeling of cancers by the Surveillance of Rare Cancers in Europe (RARECARENet) project and NCRC system. Compared with cases using the RARECARENet classification in Europe, 69 351 cases/year (6.8%) switched status with our classification, with 45 293 and 232 109 cases (4 years) switching from rare and non-rare, respectively. Major differences included diffuse large B-cell lymphomas, some thyroid cancers, oral cavity and lip cancers, and squamous cell carcinoma of the uterine cervix. As the NCRC includes newly classified tumor entities, it warrants validation using other diverse cohorts.