A growing number of clinical trials are testing Chinese acupuncture in the management of headache disorders. Little is known, however, about the relationship between International Headache Society diagnostic criteria and traditional Chinese medicine (TCM) diagnosis in primary headache disorders. We conducted a secondary analysis of the data of the prospective, controlled, blinded German acupuncture trials for migraine and tension-type headache. Data were collected from 1042 headache patients, of whom 633 were diagnosed with migraine and 409 with tension-type headache. We found that the diagnoses of migraine and tension-type headache were mirrored by different patterns of TCM diagnoses, with the patterns Liver Yang Rising, Liver Fire Rising, and Phlegm appearing to be best suited to differentiating between migraine and tension-type headache. Although not unexpected, given that the diagnosis of primary headache disorders in both diagnostic systems is based largely on the nature and quality of patient-reported symptoms, this finding suggests that migraine and tension-type headache are associated with different patterns of TCM diagnosis.