Pancreatic duct stone is thought not only to be the cause of abdominal pain but also to be a risk factor for pancreatic cancer. Several treatment options have been implemented in the treatment of pancreatic duct stones. Stone location is a critical factor in selecting treatment. We present the results of 27 endoscopic treatments and 35 surgical treatments performed in three hospitals at a single university between January 2000 and January 2005. The results were compared retrospectively in terms of success rate of stone removal, length of hospital stay, complications, pain relief, and changes of pancreatic functions. In our study, endoscopy resulted in a similar success rate of stone removal and short-term pain relief rate as the surgical approach and with a shorter length of hospital stay. However, the surgical group had a more favorable long-term clinical result, as well as a lower number of hospital readmissions at the 5-year follow-up point. Based on long-term results, surgical treatment is more effective than endoscopy.