Congenital craniovertebral junction deformities can be associated with an anomalous vertebral artery (VA). At times, the artery crosses the joint posteriorly (i.e., persistent first intersegmental artery) and is at risk during posterior approach. We report a new variant, wherein the bilateral VA coursed medially after exiting the C3 transverse foramina to lie beneath C2 pars interarticularis and enter the foramen magnum (without passing through C2 transverse foramen anywhere along its course). This is possibly a result of bilateral persistent second intersegmental arteries. It is pertinent to recognize this unusual variant to avoid VA injury, especially while inserting C2 pars/transarticular screw.