Aortic root dilatation is rare in children, and often secondary to Marfan syndrome. Aortic root replacement for children under 5-year-old is extremely rare. We experienced a case of 3-year-old boy (92cm, 12kg) with Marfan syndrome presenting dilated aortic root (the sinuses of Valsalva of 40 mm). We electively performed a valve-sparing aortic root replacement using a 24 mm Gelweave Valsalva™ graft. Although the patient required mitral valve repair due to infective endocarditis postoperatively, the recovery from the second surgery was uneventful. The patient is currently doing well at home. This case is one of the youngest children of valve-sparing aortic root replacement in the literature.