The vertebral artery (VA) is often affected by anatomical variations; however, it is usually asymptomatic and is found incidentally. Herein, we report a case of cervical cord compression caused by bilateral aberrant VAs. A 65-year-old woman presented with paroxysmal lancinating pain in the neck that later extended to the shoulders and upper arms bilaterally. Magnetic resonance imaging and computed tomographic angiography revealed an aberrant course of both VAs entering the spinal canal between the atlas and axis and compressing the cervical cord at the atlas level. Microvascular decompression was performed with transposition of the VAs, and the pain resolved immediately after the surgery. A certain number of anatomical variants of the distal VA can be explained by size variations and connection of the lateral spinal artery (LSA). Considering that an aberrant VA may correspond to an enlarged LSA, optimal transposition should be performed to prevent neurological complications.