Sarcomas with BCOR genetic alternations, formerly treated as Ewing-like sarcomas, are malignant tumors with a poor prognosis. They have been classified under the category of undifferentiated small round cell sarcomas of bone and soft tissue since 2020. There are only a few reports on surgical treatment for these sarcomas, as they are extremely rare, and no specific treatment has been established. Among them, there have been no reports on the treatment of patients with intracardiac invasion. We report herein the case of intracardiac invasion of a rare sarcomas with BCOR genetic alternations. The patient is a 14-year-old girl who presented to the hospital with a chief complaint of left upper arm pain. Computed tomography (CT) showed tumors in the left axilla and left thoracic cavity, and after biopsies of each, we diagnosed the patient with sarcomas with BCOR genetic alternations. Although chemotherapy was planned, echocardiography revealed a mobile tumor in the left atrium, we decided to perform surgical procedure before chemotherapy to reduce the risk of embolism and sudden death. The tumor invaded directly the left upper pulmonary vein and extended into the left atrium. Since right lung metastasis was suspected, we considered the en bloc tumor resection while preserving the left lung. However it was difficult because the tumor invaded into the vicinity of the lower lobe bronchus. Concerned about extracardiac seeding, we resected the tumor as much as possible intravascularly. Although there was residual tumor, chemotherapy was started immediately after surgery, and the tumor has shrunk in size. We are planning to remove the entire tumor after several courses of chemotherapy.