Pharyngeal perforation is a rare but crucial complication of transesophageal echocardiography during cardiac surgery. We herein report the case of a 72-year-old man with infective endocarditis in the aortic valve, who had a poor performance status due to congestive heart failure and brain infarction. The echo probe of the transesophageal echocardiography was detected in the anterior mediastinum after median sternotomy. Pharyngeal repair after aortic valve replacement with bioprosthetic valve, following omental wrapping was performed simultaneously. The operative course was relatively good, and the patient moved to the general ward 32 days after the surgery.