A 47-year-old woman under anti-cancer therapy for stage IV breast cancer visited our hospital for unsteadiness of gait, vertigo, and malaise, although MRI showed no abnormal findings. Three days later, she was taken to the emergency room by ambulance since she was vomiting and scarcely moving. On admission, neurological examination revealed only vertigo, and NIHSS score was 0. Laboratory examination showed slightly increasing D-dimer and elevated CA15-3 and BCA225 levels. Since MRI showed a hyperintense area in the cerebellum, she was hospitalized under the suspicion of cancer-related stroke. Enhanced CT showed no deep vein thrombosis, and transesophageal echocardiography, transthoracic echocardiography, and carotid ultrasonography did not indicate an embolic source. However, transcranial color flow imaging (TC-CFI) showed 40 microembolic signals (MES) in the basilar artery (BA) for three minutes, with no MES in the middle cerebral artery (MCA). Despite the risk of hemorrhagic transformation, heparin was started on the six day of admission. Thereafter, MRI showed no recurrence, and MES was not seen in both the MCA and BA by TC-CFI. In this case, MES decreased significantly after heparin treatment, as indicated by TC-CFI, suggesting that MES detection by TC-CFI was useful for understanding the morbid state of cancer-related stroke.