We report a case in which aortopulmonary window (APW) in combination with pulmonary atresia was diagnosed correctly in a neonate by echocardiography. Prenatal echocardiography showed progression of tetralogy of Fallot to pulmonary atresia with retrograde pulmonary perfusion, concealing the concomitant APW in fetal life. Due to intractable heart failure, primary correction was successfully performed at the age of 4 weeks (weight 2280 g).