Cardiac lipoma is extremely rare. Here we presented a unique illustrative case of interatrial septal lipoma protruding into right atrial causing symptoms in a 54-year-old male. Echocardiogram and computed tomography showed a well-shaped, giant and fixed occupying located in interatrial septum and right atrium. The only manifestation was palpitation though the mass filled almost all atrium and compressed superior vena cava. The patient received resection of the large-sized lipoma sizing 87mm in diameter and weighing ~1000g. Pathological exam demonstrated mature lipocytes and substantiated the diagnosis of lipoma. The patient did well postoperatively and symptoms were resolved.