Cerebral venous thrombosis in various clinical conditions, such as congenital heart disease (CHD) and hyper-coagulable states, have been recognized previously. However, dural sinus thrombosis in a pediatric patient with Antiphospholipid Syndrome (APLS) after the repair of a ventricular septal defect (VSD) has not been reported yet. A child who underwent an operation for the surgical repair of VSD under cardiopulmonary bypass (CPB) developed a stroke after the procedure. A cranial computer tomography (CT) scan of the patient showed dural sinus thrombosis and severe cerebral edema. APLS and CPB were thought to be the only risk factors of dural sinus thrombosis. This observation warrants attention and screening should be taken into consideration in patients with APLS who carry a higher risk for dural sinus thrombosis after CPB.