We present a case of an atrial septal defect repair under cardiopulmonary bypass in a child with factor VII deficiency. A four-year-old girl, with the diagnosis of secundum atrial septal defect, was referred to surgery. Coagulation tests showed an international normalized ratio of 2.4. Further investigations revealed deficiency of factor VII with 42% activity. Fifteen minutes before the induction of anesthesia, 20 microg/kg dose of recombinant factor VIIa concentrate was administrated. The atrial septal defect repair was performed uneventfully. Factor VII activity markedly improved to 174%, and international normalized ratio declined to 1.1 within 1.5 hours after the substitution therapy. In our case, under a low-dose substitution therapy with recombinant factor VIIa concentrate, atrial septal defect repair under cardiopulmonary bypass was performed safely in a child with moderate congenital factor VII deficiency.