Unilateral pulmonary artery hypoplasia (UPAH) is a rare disease in adults and is frequently accompanied by a congenital cardiac anomaly at a young age. The diagnosis is usually based on computed tomography (CT), angiography, and magnetic resonance imaging (MRI). However, no reports are available on retrograde flow in patients with UPAH. We describe a 68-year-old man with isolated UPAH and retrograde blood flow. He was admitted for dyspnea on exertion for the past 23 years. His diagnosis was delayed, as his symptoms and signs mimicked his underlying pulmonary diseases, such as emphysema and previous tuberculous pleurisy sequelae. A discrepancy was detected between the results of a ventilation-perfusion scan and the CT image. This was resolved by MRI, which showed retrograde blood flow from the right to the left pulmonary artery. Using MRI, we diagnosed this patient with isolated pulmonary artery hypoplasia and retrograde flow.