We report of a case of a 44-year-old woman with a vaginal cloacagenic carcinoma who initially presented with a hymenal lesion that metastasized first to the perihilar lymph nodes and then consequently to the right ventricle. The embryological tumor is rare with only a few cases of vaginal or vulvar involvement. We present the first case of cloacagenic cancer of the vagina with metastasis to the heart. The lesion was surgically resected after completion of neoadjuvant therapy. Herein we present this unique case and the clinical manifestations of intracardiac and pericardial lesions from gynecologic malignancies.