Abdominal lymphangioma is a rare tumor in adults. The most common location is the mesentery, but this tumor occasionally develops in the pancreas. We report a case of pancreatic lymphangioma associated with blue rubber-bleb nevus syndrome (BRBNS) in a Japanese woman. The pancreatic lymphangioma spread extensively throughout the retroperitoneum without causing any symptoms for more than 4 years after its histological diagnosis by laparoscopic biopsy. Multiple hemangiomas were also seen in the mucous membranes and on the skin. The hemangiomatosis was segregated in the dominant fashion in her family, and a germ-line gain-of-function mutation (Arg849Trp) in TIE2 gene was confirmed. To our knowledge, this is the first report of pancreatic lymphangioma occurring in association with BRBNS in a patient with genetic alteration. We describe the clinical features of this case and discuss a possible correlation between these two uncommon conditions.