Piriform fossa and/or esophageal injuries caused by calibration tubes are relatively rare and remain unelucidated. Herein, we report the case of a 36-year-old woman with morbid obesity, sleep apnea, and menstrual abnormalities who was scheduled to undergo laparoscopic sleeve gastrectomy (LSG). We inserted a 36-Fr Nelaton catheter made of natural rubber as a calibration tube during the surgery. However, excessive resistance was observed. We confirmed a submucosal layer detachment approximately 5 cm from the left piriform fossa to the esophagus using intraoperative endoscopy. Additionally, LSG was performed using an endoscope as the guiding calibration tube. We inserted a nasogastric tube under endoscopy with a guidewire before completing the surgery, hoping for a guiding effect on the saliva flow. After 17 months, the patient had successfully lost weight postoperatively without complaints of neck pain or discomfort during swallowing. Therefore, in cases where the damage is limited to the submucosal layer, as in this case, conservative therapy should be considered; this is similar to the concept of endoscopic submucosal dissection not requiring suture closure. This case highlights the risk of iatrogenic injuries to the piriform fossa and/or esophagus during LSG and the importance of careful calibration tube insertion to prevent them.