Three cases of rare complications after Fontan operation were retrospectively analysed. Two cases experienced complication of protein-losing enteropathy, among whom one was diagnosed as asplenia with single ventricle and pulmonary stenosis, and the other was diagnosed as functional single ventricle with pulmonary hypertension. The other case had complication of plastic bronchitis, who was diagnosed as congenital corrected transposition of the great arteries with ventricular septal defect and pulmonary stenosis. Time intervals between Fontan operation and occurrence of complications were 3 weeks, 3 months, and 5 months respectively. One patient died after operation, and 1 patient lost in follow up. The increased systemic venous pressure, low cardiac output and high pulmonary resistance may be possible mechanisms of protein-losing enteropathy and plastic bronchitis.