Endoscopic thyroidectomy is being performed increasingly, because it is less invasive and more cosmetically advantageous, and thus improves the postoperative quality of life. However, the technical aspects of this procedure can increase the risk of certain complications, which include subcutaneous emphysema, hypercarbia, pneumothorax, and pneumomediastinum. This report describes the case of a 37-year-old female patient who had subcutaneous emphysema and hypercarbia due to increased carbon dioxide absorption during endoscopic thyroidectomy. After increasing minute ventilation, paying cautious attention to signs of other complications, the operation proceeded and blood gas findings improved. The operation ended successfully and she showed no further problems.