Background The formation of a dural arteriovenous fistula (DAVF) at the craniocervical junction is rare. Such a fistula can be fed by the branches of the vertebral and external carotid arteries. The lateral spinal artery can branch from the vertebral artery. The feeders of a DAVF at the craniocervical junction are often diagnosed on preoperative angiography, and there is little reported evidence on the intraoperative diagnosis of the lateral spinal artery. Case description An 84-year-old man presented with motor weakness and sensory disturbance of the lower extremities. Edematous changes in the medulla oblongata and cervical spinal cord were observed on magnetic resonance imaging. Cerebral angiography revealed a DAVF fed by a branch of the vertebral artery, with a shunting point located in the dura of the right condyle; the main drain was the anterior spinal vein. The DAVF drain was surgically obliterated to prevent hemorrhagic events and improve neurological symptoms. Intraoperatively, an artery branching from the feeder of the DAVF was identified and preserved. The patient had a good postoperative course, and the neurological symptoms were ameliorated. Follow-up cerebral angiography revealed proximal branching of the lateral spinal artery from the feeding artery of the DAVF. Conclusion A lateral spinal artery was identified intraoperatively while a DAVF at the craniocervical junction was obliterated. This suggests that preoperative imaging should be carefully reviewed, and endovascular procedures should consider such possibilities to avoid adverse ischemic outcomes.