Chronic esophageal achalasia can lead to significant morphological changes in the esophagus, posing challenges during endoscopic examinations. Here, we report a case of iatrogenic esophageal perforation in an elderly patient with achalasia. An 80-year-old woman presented with severe dysphagia and marked weight loss, indicating chronic malnutrition. She had a 50-year history of achalasia, previously treated with a Heller-Dor operation. Endoscopic evaluation was performed to assess the esophageal condition; however, during the procedure, an iatrogenic perforation occurred. The patient underwent urgent management under general anesthesia. Two drainage tubes were placed at the base of the right thoracic cavity. Saline infusion via the perforation site enabled endoscopic lavage of the thoracic cavity. The perforation was initially closed with the thread-and-clip technique. After 30 days, the perforation site had developed into a fistula approximately 1 cm in size. Attempts to close it using argon plasma coagulation ablation and over-the-scope clip were unsuccessful. It was presumed that the significant accumulation of fluid in the esophagus due to achalasia was hindering fistula closure. Consequently, peroral endoscopic myotomy was performed, ultimately leading to the closure of the fistula. Despite requiring prolonged hospitalization for recovery and nutritional rehabilitation, the patient was eventually discharged in stable condition, able to consume meals without difficulty. This case underscores the high risk of esophageal perforation during endoscopy in elderly patients with advanced achalasia and subsequent malnutrition. Furthermore, it highlights the potential for successful management of severe complications like esophageal perforation through advanced endoscopic techniques, thereby avoiding the need for surgical intervention.