Carbon dioxide (CO₂) embolism is a rare but potentially life-threatening complication of laparoscopic procedures. Although endoscopic thyroidectomy using CO₂ gas insufflation appears to be superior to conventional open thyroidectomy in terms of cosmetic results, it may cause venous or fatal paradoxical CO₂ embolism. We report a case of paradoxical CO₂ embolism during CO₂ gas insufflation in an endoscopic thyroidectomy that was confirmed by transesophageal echocardiography (TEE). Paradoxical embolization via transpulmonary right-to-left shunting of venous CO₂ gas emboli was revealed by TEE examination. The patient recovered without complications. In conclusion, although endoscopic thyroidectomy is a promising approach that is gaining popularity and offers excellent cosmetic results compared with conventional open thyroidectomy, this case report emphasizes the importance of anticipating and being vigilant for potential CO₂ embolism.