Congenital partial aplasia of the atlas with a posterior arch remnant is rare. It may be found as an incidental radiological finding or patients can present with neurological signs and symptoms after head or neck trauma. A 36-year-old female presented with a 3-day history of right sided neck pain radiating down the right arm. Radiographs of the cervical spine showed a radiolucent area in the region of the posterior arch of the atlas. Computed tomography subsequently revealed partial absence of the posterior arch of the atlas with a defect at the anterior ring. Her clinical condition subsequently improved with rest, analgesia and physiotherapy. This case report illustrates a situation where congenital defect of the posterior arch of the atlas was revealed in a patient with neck pain. Awareness of the existence of this condition will help clinicians avoid misdiagnosis and excessive investigations.