Objective　To explore the clinical features of systemic onset of juvenile idiopathic arthritis (SoJIA) with atlantoaxial subluxation as the initial manifestation. Methods　The clinical data from one SoJIA patient with atlantoaxial subluxation as the initial manifestation were retrospectively analyzed. Results 　A 9-year-old boy presented the head and neck movement disorder as the first symptom, developed fever on the third day, then rapidly progressed on 23rd day, with a sharp decline in red blood cell, platelet, and hemoglobin, blood coagulation dysfunction, and a large number of bilateral pulmonary exudation. Ultrasonography showed excess fluid in abdomen, chest, and pericardium. According to the 2001 version of the revised International College of Rheumatology standard, the diagnosis of SoJIA combined macrophage activation syndrome was confirmed. Then treated with hemoperfusion, filtration, and methylprednisolone combined with cyclosporine A, the disease was in remission. Conclusion　 For children with spontaneous atlantoaxial subluxation accompanied by the systemic symptoms, with no obvious skeletal deformity or acute inflammation etc., should be alerted to the consideration of systemic juvenile idiopathic arthritis.