Background and objectives Prophylactic pancreatic duct stent placement effectively reduces post-endoscopic retrograde cholangiopancreatography pancreatitis in high-risk patients, but the optimal stent remains unclear. We modified a 5-Fr, 3 cm pancreatic stent by removing the flange on the pancreatic side and compared the rate of spontaneous dislodgement and complications with the ordinary stent. Methods This was a randomized controlled trial at six tertiary endoscopic centers. Patients deemed high risk for post-endoscopic retrograde cholangiopancreatography pancreatitis randomly received modified or ordinary pancreatic stent. The primary outcome was spontaneous stent dislodgement at five days and 14 days. Secondary outcomes were the success rate of stent placement and complications. Results A total of 276 patients were randomly assigned to receive modified stents (mS group) and ordinary stents (oS group). The placement of a pancreatic stent was successful in all 276 patients. There were no significant differences between groups with respect to age, sex, major diagnosis, or indications for stenting. At five days the spontaneous dislodgement rate was 47.72% for the mS group and 15.67% for the oS group ( p<0.001); at 14 days the rates were 84.21% and 42.65%, respectively ( p < 0.001). Post-endoscopic retrograde cholangiopancreatography pancreatitis occurred in 6.52% of all patients. There were no significant differences regarding the incidences of post-endoscopic retrograde cholangiopancreatography pancreatitis, hemorrhage or fever. Conclusions The modified short 5-Fr stent has a higher spontaneous dislodgement rate than ordinary pancreatic stent, thus obviating the need for endoscopic removal. The modified pancreatic stent does not increase the incidence of post-endoscopic retrograde cholangiopancreatography pancreatitis or other complications. The endoscopist can consider removing the flange on the pancreatic duct side for prophylactic pancreatic duct manipulation.