In cases after pancreas transplantation (PTx), the pancreas graft might be lost for various reasons, including a pancreatoduodenal graft-related complication or patient death with a functioning graft. Although the causes seem to have distinct characteristics, the causes of pancreas graft loss have not been characterized. This study aimed to characterize the causes of pancreas graft loss by analyzing data from a Japanese nationwide registry. This study included 391 patients who received simultaneous pancreas-kidney transplantation among 461 patients with PTx during the study period in approved institutions in Japan. We characterized each cause in terms of the timing of the cause-specific graft loss and preoperative factors associated with graft loss based on nationwide data from a Japanese nationwide registry. Among the 391 cases, 113 lost the pancreas graft due to patient death with a functioning graft (DWFG; n = 34, 44.2%), graft thrombus (n = 22, 28.6%), or chronic rejection (CR; n = 7, 9.1%). Average (± standard deviation) time from PTx to graft loss due to DWFG, graft thrombus, and CR was 3.70 ± 4.36, 0.02 ± 0.01, and 2.37 ± 2.08 years, respectively. Duration of type 1 diabetes mellitus and donor body mass index were significantly associated with pancreas graft loss due to DWFG and graft thrombus, respectively. This characterization showed that the timing and preoperative factors associated with pancreas graft loss were significantly different for different causes of graft loss. These results may inform PTx follow-up protocols to ensure that appropriate care is based on the cause of graft loss.