Post-transplant patients reportedly have a higher risk of de novo neoplasms. However, intraductal papillary mucinous neoplasm (IPMN) of the native pancreas after pancreas transplantation (PTx) has not been well investigated. The choice of treatment, especially invasive treatment, for de novo neoplasms in transplant patients should consider their impaired immunity. In this context, we present a case of IPMN developing in the native pancreas of a PTx patient. A 53-year-old man underwent a follow-up abdominal computed tomography scan 6 years after a simultaneous pancreas-kidney transplant for type 1 diabetes mellitus with end-stage diabetic nephropathy requiring hemodialysis. The scan revealed IPMN in the pancreas head; an enhancing internal solid component suggested a high risk of malignancy, indicating surgical resection. Partial pancreatectomy or pancreaticoduodenectomy was anatomically indicated, but considering the insulin-secreting ability of the transplanted pancreas and the potential high risk of postoperative pancreatic fistula due to immune impairment after partial pancreatectomy, total pancreatectomy (TP) was performed. The patient is alive with good pancreas graft function, no signs of indigestion for 18 months after TP, and no evidence of IPMN recurrence. This report should help clinicians characterize de novo IPMN in the native pancreas and determine IPMN therapeutic options for transplant patients.