Background: Endoscopic therapy and surgery are both conventional treatments to remove pancreatic duct stones that developed during the natural course of chronic pancreatitis. However, few studies comparing the effect and safety between surgery drainage and endoscopic drainage (plus Extracorporeal Shock Wave Lithotripsy, ESWL).The aim of this study was to compare the benefits between endoscopic and surgical drainage of the pancreatic duct for patients with calcified chronic pancreatitis. Methods: A total of 86 patients were classified into endoscopic/ESWL (n = 40) or surgical (n = 46) treatment groups. The medical records of these patients were retrospectively analyzed. Results: Pain recurrence and hospital stays were similar between the endoscopic/ESWL treatment and surgery group. However, endoscopic/ESWL treatment yielded significantly lower medical expense and less complications compared with the surgical treatment. Conclusions: In selective patients, endoscopic/ESWL treatment could achieve comparable efficacy to the surgical treatment. With lower medical expense and less complications, endoscopic/ESWL treatment would be much preferred to be the initial treatment of choice for patients with calcified chronic pancreatitis.