We observed a rare anatomical variation of a persistent first intersegmental vertebral artery in the C1-C2 region in an elderly Chinese male cadaver at Changzhi Medical College. In this case, the vertebral artery, rather than passing through the transverse foramen of the atlas, exits the transverse foramen of C2 and enters the spinal canal at the lower portion of the C1 posterior arch. The original transverse foramen of C1 was filled with connective tissue. This report details the anatomical characteristics of this abnormal vertebral artery and discusses its anatomical, surgical, and developmental implications. We describe the detailed morphological features of a rare VA variant and discuss the anatomical, clinical, and developmental aspects of this case. A case of head dissection. The anatomical characteristics of the VA were studied and documented, and anatomical measurements were collected. In this case, the vertebral artery, rather than passing through the transverse foramen of the atlas, exits the transverse foramen of C2 and enters the spinal canal at the lower portion of the C1 posterior arch. The original transverse foramen of C1 was filled with connective tissue. The anomalous development of segmental arteries in our case is linked to failures in the embryonic sclerotome reconstruction during development and failure.