Spontaneous spinal epidural hematoma (SSEH) is considered to be a relatively rare disease that can result in serious neurological sequelae. The pathogenesis and risk factors of SSEH are still unknown, and its differential diagnosis varies widely. Misdiagnosis with more common conditions such as stroke or aortic syndromes can occur. We report the case of a 27-year-old man who developed sudden upper back pain with no specific precipitant. Five days later, he visited our emergency department complaining of weakness in both lower limbs and dysuria. He had a history of intracardiac repair and a Blalock-Park procedure for an interrupted aortic arch and ventricular septal defect in infancy. Additionally, he had undergone an aortic root dilatation and aortic valve replacement at the age of 10 because of progression of aortic and supra-aortic stenosis and had received chronic anticoagulation and antiplatelet therapy with warfarin and aspirin, respectively. An emergency spine magnetic resonance imaging scan indicated a mass at the Th3-Th5 level with severe compression of the dural sac and the spinal cord. Emergency excision showed a spinal epidural hematoma. Mild postoperative gait disturbance and dysuria persisted, requiring rehabilitation and intermittent self-urethral catheterization. As patients with adult congenital heart disease have an increased risk of bleeding, they may be at risk of developing SSEH. However, this is the first report to describe such an association.