Identifying the cause of death is important for the study of end-of-life patients using claims data in Japan. However, the validity of how cause of death is identified using claims data remains unknown. Therefore, this study aimed to verify the validity of the method used to identify the cause of death based on Japanese claims data. Our study population included patients who died at two institutions between January 1, 2018 and December 31, 2019. Claims data consisted of medical data and Diagnosis Procedure Combination (DPC) data, and five definitions developed from disease classification in each dataset were compared with death certificates. Nine causes of death, including cancer, were included in the study. The definition with the highest positive predictive values (PPVs) and sensitivities in this study was the combination of “main disease” in both medical and DPC data. For cancer, these definitions had PPVs and sensitivities of > 90%. For heart disease, these definitions had PPVs of > 50% and sensitivities of > 70%. For cerebrovascular disease, these definitions had PPVs of > 80% and sensitivities of> 70%. For other causes of death, PPVs and sensitivities were < 50% for most definitions. Based on these results, we recommend definitions with a combination of “main disease” in both medical and DPC data for cancer and cerebrovascular disease. However, a clear argument cannot be made for other causes of death because of the small sample size. Therefore, the results of this study can be used with confidence for cancer and cerebrovascular disease but should be used with caution for other causes of death.