Background: To investigate the present situation of emergency headache in many general hospitals in Chongqing Province, China.Methods: From January 1 to December 31, 2017, we studied patients who complained of headaches as the main symptom in the emergency department of 17 general hospitals in Chongqing Province. Each patient with a headache was interviewed and the medical history was collected by administering a questionnaire. The diagnosis of headache is based on the third edition of the International Classification of Headache Disorders (ICHD-3 beta). Results: In 2017, 16434 patients complained of headache in 17 general hospitals in Chongqing, accounting for 2.3% of all emergency patients. Eight thousand one male patients (48.7%) and 8433 female patients (51.3%) experienced a headache. The average age was (41.8 ± 13.2) years, and the course of disease was 3 hours to 15.2 years. Regarding the initial diagnosis, 7299 patients (44.4%) were diagnosed secondary headache, 5076 (30.9%) were diagnosed with primary headache and 4059 (24.865%) could not be diagnosed. The hospitalization rates for these patients were 60.3%, 12.2%, and 41.5%, respectively. Migraine is still the most common type of primary headache. Conclusions: This study shows that the misdiagnosis rate and missed diagnosis rate of patients with an emergency headache are high, and the emergency department still performs overtesting and hospitalizations.