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Abstract Background Patients with Marfan syndrome commonly require spinal deformity surgery. The purpose of this case report is to present a rare thoracotomy complication. We present the management of such a patient. Case summary In a known case of Marfan syndrome, an 18-year-old Persian man was admitted to our hospital with scoliosis. The patient underwent radiological examinations, and thoracic scoliosis of 70° was diagnosed. A right thoracotomy for anterior spinal fusion from the sixth rib and posterior spinal fusion were performed successfully. Two months later, he was readmitted because of winging of the right scapula due to serratus anterior palsy. Electromyography and nerve conduction velocity confirmed long thoracic nerve injury. Conservative treatment was provided. Ultimately, the patient recovered completely in the last follow-up visit 6 months after the surgery. Discussion This is the first report of ipsilateral winged scapula after thoracotomy. Attention needs to be paid to surgical techniques in patients with Marfan syndrome.