A 25-year-old woman was admitted to our hospital with chest pain and dyspnea, and was diagnosed as having a right atrial myxoma complicated with pulmonary embolism. An emergency operation was performed with cardiopulmonary bypass. A papillary pedunculated tumor was found having a narrow-based attachment to the free atrial wall. After the tumor was carefully removed together with the atrial wall around the attachment, pulmonary embolectomy was performed. Several fragments of the tumor were removed, and sufficient back-flow from the pulmonary artery was established. The postoperative course was uneventful. However, a non-perfused area was observed in the left lower lung on pulmonary hemodynamic scintigraphy at 3 months after the operation. Long-term observation is required due to the high risk for metastasis and recurrence, and further surgical treatment remains the most appropriate treatment option. A second operation may be needed to prevent progression in complications.