The patient was a seven-old-boy with univentricular heart of left ventricular morphology with transposition of the great arteries and coarctation of the Aorta. Pulmonary artery banding and coarctactomy (subclavian flap method) were performed as prior surgery during infancy and significant subaortic stenosis (SAS) was not identified before or immediately after Fontan operation. SAS was suspected in an ejection murmur that developed without symptoms two years and five months after Fontan operation. It became clear that the SAS was caused by both restrictive ventricular septal defect and narrowing of outlet chamber (right ventricle). Surgery was performed with myectomy in the outlet chamber, enlargement of ventricular septal defect and a patch enlargement of the right ventricle outflow tract for relief of the SAS. Postoperative pressure gradient across the subaortic component was decreased, however, valve regurgitation remained grade I to II. The mechanisms of SAS after Fontan operation are related to hypertrophy of the subaortic component that incorporates the infundibulum and trabeculae. Careful morphological investigation is essential in patients with risk factors for SAS Mild deterioration of the ventricular compliance due to progressive SAS may result in reduction of the cardiac function and patient's quality of life. Adequate surgical treatment to relieve the SAS is considered essential before and after Fontan operation.