Perimedullary arteriovenous fistulas (AVFs) at the craniocervical junction are uncommon, and are often fed by the anterior spinal artery, with only a few cases fed by the intradural vertebral artery (VA). A 55-year-old man presented with a case of perimedullary AVF fed by the VA at the craniocervical junction manifesting as subarachnoid hemorrhage. Left vertebral angiography demonstrated an AVF supplied by branches from the VA. Three-dimensional computed tomography angiography (3D-CTA) revealed that the feeding arteries originated from the VA at the intradural position. Two feeding arteries were coagulated and dissected, followed by coagulation of a small feeder. The draining veins became discolored and shrank. 3D-CTA performed 2 months after the operation revealed disappearance of the AVF. Open surgery was successfully performed for the almost perimedullary AVF at the craniocervical junction, and is considered to be preferable for the treatment of this disease.