A 66-year old hypertensive man having a prostate cancer was admitted to our hospital with sudden onset right hemiparesis. On admission, he showed left hemiplegia, hypesthesia, right limb ataxia, and dysarthria. The NIHSS score was 16. Diffusion weighted magnetic resonance imaging showed an acute infarct in the middle pons and magnetic resonance angiography (MRA) revealed basilar artery (BA) occlusion. Carotid Doppler ultrasonography showed distal occlusion pattern of the bilateral vertebral artery. He was treated with intravenous rt-PA at 116 minutes after symptom onset. One hour later, his symptom was not improved and BA was still occluded on follow-up MRA. Therefore, we performed mechanical thrombectomy with Merci(®) Retrieval System. At 323 minutes after onset, BA was successfully recanalized and NIHSS score decreased to 4 without hemorrhagic complication. Medication of oral warfarin was started on day 19 because paroxysmal atrial fibrillation was detected by electrocardiogram. The retrieved thrombus was pathologically diagnosed as a organizing mixed thrombus probable cardiac origin. On day 27, he was discharged home without any neurological deficit. Additional thrombectomy with Merci(®) Retrieval System is a promising treatment strategy for BA occlusion which is resistant to intravenous rt-PA thrombolysis.