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Complications may arise following an endoscopic thoracic sympathectomy; however, these are rare. Here, we report a case of isolated damage to a muscle branch of the lateral pectoral nerve in a patient who underwent endoscopic thoracic sympathectomy to treat hyperhidrosis. Eight weeks after the operation, the patient came to our clinic complaining of numbness and a tingling sensation in the left anterior chest wall, with asymmetric atrophy in the left areolar area. We performed a nerve conduction study and needle electromyography for suspected brachial plexopathy or pectoral nerve injury. These results showed an isolated left lateral pectoral nerve injury, which we attributed to the endoscopic thoracic sympathectomy. This is the first case to report an isolated lateral pectoral nerve injury after endoscopic thoracic surgery.