||Traditional acupuncture (TA) and ear acupuncture (EA) are used for treatment of headache, trigeminal neuralgia, and retro-auricular pain. The purpose of this study is to develop effective treatment using combined acupuncture (CA) which consists of TA and EA and to set clinical protocols for future trials. Participants were divided into TA (n = 15) control and CA (n = 34) experimental groups. Obligatory points among Korean Five Element Acupuncture and optional individual points along with symptom points were used in the TA group. The CA group was exposed to ear points of Fossion and TA. Acupuncture treatment consisted of six mandatory sessions per patient over 3 weeks and extended to 12 sessions. Pain was assessed using the visual analogue scale. We compared TA to CA and researched their relevant publications. No significant difference was observed between the two groups (p = 0.968) which showed pain-alleviating tendency. Pain alleviation was significantly different after the fifth and sixth sessions (p = 0.021, p = 0.025), with headache being the most significantly relieved (F = 4.399, p = 0.018) among the diseases. When assessing pain intensity, both the Headache Impact Test and the Migraine Disability Assessment Scale should be adopted for headache and the fractal electroencephalography method be used in pain diseases. In the future, studies should consist of TA, EA, and CA groups; each group having 20 patients. Treatment number should to be no less than 10 sessions. Korean Five Element Acupuncture should be a compulsory inclusion along with individual points being optional inclusion in TA. EA could be selected from Nogier, Fossion and so forth. In conclusion, acupuncture treatment, whether TA or CA, showed pain alleviation in headache, trigeminal neuralgia, and retro-auricular pain, but no significant difference was seen between groups. Prospective, well-controlled, and relevant protocols using multimodal strategies to define the role of TA, EA, and CA are needed.