The present study was comprised of 43 patients (16 men) with cervicogenic headaches for over three months, diagnosed according to the International Classification of Diagnostic Criteria of Headaches (ICDH-II). The patients were randomly assigned to receive either manual therapy for the cervical region (usual care group) or additional manual therapy techniques to the temporomandibular region to additionally influence temporomandibular disorders (TMD). All patients were assessed prior to treatment, after six sessions of treatment, and at a six-month follow-up. The outcome criteria were: intensity of headaches measured on a colored analog scale, the Neck Disability Index (Dutch version), the Conti Anamnestic Questionnaire, noise registration at the mandibular joint using a stethoscope, the Graded Chronic Pain Status (Dutch version), mandibular deviation, range of mouth opening, and pressure/pain threshold of the masticatory muscles. The results indicate in the studied sample of cervicogenic headache patients, 44.1% had TMD. The group that received additional temporomandibular manual therapy techniques showed significantly decreased headache intensities and increased neck function after the treatment period. These improvements persisted during the treatment-free period (follow-up) and were not observed in the usual care group. This trend was also reflected on the questionnaires and the clinical temporomandibular signs. Based on these observations, we strongly believe that treatment of the temporomandibular region has beneficial effects for patients with cervicogenic headaches, even in the long-term.