We report an extremely rare case involving a posterior arch anomaly of the atlas, causing a vertebral artery dissection (VAD) induced posterior circulation stroke. A 16-year-old girl was admitted to hospital because of new onset dizziness. VAD related multiple infarction in the posterior circulation was revealed. The congenital posterior arch anomaly of the atlas, along with instability of the atlantoaxial joint, were discovered accidentally during follow-up. This is the first case of ischemic stroke related to atlantal posterior arch aplasia and atlantoaxial instability. Although rare, it reminds us that investigation of the craniovertebral junction should be considered when stroke occurs in young patients.