A 74-year-old man had been taking warfarin for atrial fibrillation, but warfarin was discontinued due to upper gastrointestinal bleeding. One week later, left hemiplegia occurred, and cranial magnetic resonance imaging revealed multiple cerebral infarctions. Systemic examination revealed thrombi in both atria as well as duodenal cancer. Because all of the thrombi in both atria were larger than 30 mm in diameter, the risk of embolism or sudden death was assumed to be high. Although the use of cardiopulmonary bypass for cancer patients is controversial, bilateral atrial thrombectomy was performed 4 weeks after cerebral infarction onset because reasonable survival duration was expected with surgery for duodenal cancer after thrombectomy and further treatment. The timing of and indications for surgery in this case are discussed.