Endoscopy is commonly used in patients undergoing Roux-en-Y gastric bypass (RYGBP) for diagnosis and intervention. Stomal stricture at the gastrojejunostomy occurs in approximately 3% to 17% of patients after laparoscopic RYGBP. The incidence of iatrogenic perforation during stomal balloon dilatation is reported to be 3% to 12% among these patients. Surgery has typically been required for iatrogenic perforation. With the availability of the endoclip, endoscopists are able to manage iatrogenic perforation non-operatively. We report a patient who had jejunal perforation during balloon dilatation after RYBGP, who was successfully closed with endoclip applications and managed non-operatively.