An one-year old girl, who had pulmonary artery (PA) banding and balloon atrioseptostomy done in the newborn period, underwent modified Fontan procedure on an emergency basis without cardiac catheterization, because of right heart failure. Echocardiogram showed no subaortic stenosis at Fontan procedure. Five years later, subaortic stenosis was documented with a 65 mmHg of ventricular-aortic pressure gradient at catheterization. A modified Damus-Kaye- Stansel (D-K-S) procedure was successfully performed using an end-to-end anastomosis of the distal aorta and a common stump, consisting of previously suture-closed main PA stump and the proximal aorta. At postoperative catheterization, the pulmonary valve was functioning well at LV outlet portion without regurgitation and stenosis. Significant subaortic stenosis may develop after Fontan procedure in patients with morphological narrowing without demonstrable pressure gradient. Such patients should have surgical intervention to the narrowing at the time of Fontan procedure. The modified D-K-S procedure can be an effective procedure to relieve subaortic stenosis after Fontan procedure.