Prothrombin G20210A mutation is an important prothrombotic condition for venous thrombosis. Recently, some studies have also considered it to be a risk factor for arterial ischemic stroke in children. A 10-year-old boy with basilar artery thrombosis who was heterozygous for prothrombin G20210A mutation is described. In concordance with the previous literature, the present case suggests that prothrombin G20210A mutation may be a risk factor for arterial ischemic stroke in childhood.