A 27 year-old woman with congenitally corrected transposition of the great arteries (ccTGA), which had been diagnosed five years previously, was admitted to our department because of severe heart failure and a suspected left ventricular thrombus. During the emergency operation, thrombi were removed from the left ventricle and tricuspid annuloplasty was performed. To the best of our knowledge, this is the first case report describing thrombus formation in the pulmonary ventricle in a patient with ccTGA. Most probably, the coexistence of multiple risk factors contributed to the thrombus formation.