The pancreatic duct stenting is now recognized as the treatment option for a number of pancreatic disorders. Although the stent-induced ductal changes may result, there is little information regarding the frequency of these stent-induced changes in chronic pancreatitis. Pancreatic stents may occlude with time, but there is only little information available on the nature of the clogging process. Although a short-term efficacy of endoscopic pancreatic duct stenting has been proved, the long-term efficacy continues to be controversial. The aim of this study was to report a case of chronic pancreatitis with pancreatolith after the incidental long-term pancreatic stenting for 3 years due to a pancreas divisum with acute pancreatitis. Also, this study described the analysis of the ultrastructural changes in the surface of an occluded pancreatic stent. A scanning and transmission electron microscopy showed an amorphous protein matrix in whole stent that arranged as a network in some areas but arranged as the layers in other areas. A variable number of bacteria of mixed species, calcium carbonate or calcium oxalate crystal, round leukocyte were scattered in the protein matrix. The yeast and plant material were seen in some part of the stent as well.