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Background: An 8-year-old girl had severe neck pain and stiffness after trauma. CT scan showed atlantoaxial rotatory subluxation (AARS). She had conservative treatment because she did not have neurological symptoms and spinal basilar artery dysfunction. Conservative therapy was halter traction twice for 4 weeks. However, pain and stiffness persisted. She had been recommended to have surgery from her physician, but she received manual therapy for non-surgical procedures. Methods: The joint mobilization, muscle energy technique, motor control exercise, and deep neck flexor (DNF) endurance exercise were applied as manual therapy and 10 session for 2weeks. Results: Clinical outcomes were measured at initial baseline, after 2 weeks, and after 6weeks. Active range of motion was completely restored after 6weeks and numeric pain rating scale was completely reduced after 2 weeks. The strength of neck flexor muscle recovered to normal after 2 weeks, and the DNF endurance was improved to 25 seconds after 2 weeks and to 42 seconds after 6weeks. Motor control capacity recovered to 30 ㎜Hg after 2 weeks. Conclusions: This case report describes the immediate and short-term clinical outcomes for a patient presenting with symptoms of neck pain following AARS. Clinical rationale and patient preference aided the decision to incorporate manual therapy as a treatment for this patient. Manual therapy has shown a successful recovery in AARS patients, more research is needed to validate the inference of this case report.