Abstract Background Central venous catheter (CVC) is often used in the perioperative management of esophageal cancer. The position of the CVC tip has been reported to shift with body positioning and, although infrequent, may traverse into the azygos vein arch. Herein, we describe a case where a migrated CVC tip in the azygous vein arch was identified during esophageal cancer surgery, preventing CVC dissection concurrent with azygous vein arch resection. Case presentation A 65-year-old man was diagnosed with advanced esophageal cancer and was referred to our department for surgery after undergoing neoadjuvant chemotherapy. He underwent robot-assisted subtotal esophagectomy, followed by gastric conduit reconstruction via the posterior sternal route. Thoracic manipulation was performed with the patient in the prone position. During the surgery, a foreign body was found in the azygos vein arch, indicating that a central venous catheter had inadvertently entered the azygos vein arch. The catheter was retracted by 5 cm, and after confirming that no catheter remained in the azygos arch, the azygos vein arch was separated using an autosuture device. Conclusions Central venous catheter migration can occur in a various vessels. During prone esophageal cancer surgery, elevating the right upper extremity may alter the catheter tip’s position from its the preoperative position. CVC amputation should be observed because the azygos vein arch is often amputated to facilitate upper mediastinal dissection during esophageal cancer surgery.