Chlamydia psittaci (C. psittaci) pneumonia with headache as the initial symptom is very rare. This paper reports a patient, whose initial symptom was headache, successively presented clinical manifestations such as high fever, cough, expectoration and dyspnea. Chest CT showed lung infection. C. psittaci pneumonia was diagnosed by metagenomic next-generation sequencing technology combined with avian exposure history. After treated with doxycycline and moxifloxacin, patient's condition improved. Based on literature review, this study explores the clinical characteristics, auxiliary examinations, as well as diagnosis and treatment plans of C. psittaci pneumonia. It aims to improve clinicians' understanding on C. psittaci pneumonia with headache as the initial symptom, so as to conduct early diagnosis and treatment, as well as to avoid misdiagnosis and missed diagnosis.