Foramen magnum dural arteriovenous fistula (DAVF) is a rare disease, with some reported cases of successful treatment. We achieved complete obliteration of the foramen magnum DAVF through microsurgery after complications of endovascular embolization. We reviewed the treatment modalities and outcomes, focusing on pathologic and anatomic features from the literature. A 65-year-old man was admitted to our hospital with sudden diplopia. Magnetic resonance imaging revealed a subarachnoid hemorrhage around the right side of the prepontine cistern, and a foramen magnum DAVF was diagnosed by angiography. Subsequent angiography revealed that the fistula was supplied by the right neuromeningeal trunk of the ascending pharyngeal artery and the right posterior meningeal artery of the vertebral artery (VA), and the veins of the pouch via the fistula were retrogradely draining into the intracranial veins. We aimed to treat complete occlusion endovascularly with balloon-augmented transarterial Onyx injection via the posterior meningeal artery, but Onyx was refluxed to the VA through the anastomosis between the VA and posterior meningeal artery. Onyx subsequently migrated to the top of the basilar artery, causing occlusion, so we urgently removed the Onyx with a stent retriever (Trevo). Several weeks later, we performed complete obliteration of the foramen magnum DAVF via a lateral suboccipital approach with a C1 laminectomy. Most foramen magnum DAVFs were obliterated completely with only endovascular treatment. Microsurgery is an effective and reliable treatment for incomplete occlusion and complications.