The ratio of correct diagnosis for primary headache has always been relatively low for general practitioners due to the unacquaintance with headache guideline in Chinese primary hospitals. This study proposed a computerized headache guideline method using SAGE module and developed a decision support system for headache diagnosis, which could be expected to help general practitioners of primary hospitals improve diagnostic accuracy. 282 previously diagnosed cases from EMR were used to evaluate the diagnostic accuracy of the system, the result is: migraine 144/153 (94.1%), tension-type headache 89/100 (89.0%), cluster headache 10/11 (90.9%) and chronic daily headache 53/57(93.0%). The proposed system is in the starting phase of the implementation at the outpatient department of Neurology in Chinese PLA general hospital.