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OBJECTIVE To compare the long-term effect of adding real or sham dry needling with conventional physiotherapy in cervicogenic headache. DESIGN A randomized controlled trial. SETTING Physiotherapy Clinic, Rouhani Hospital of Babol University of Medical Sciences, Iran. SUBJECTS Sixty-nine patients with cervicogenic headache. METHODS Patients were randomly assigned into a control group (n = 23) receiving conventional physical therapy; a dry needling group (n = 23) receiving conventional physical therapy and dry needling on the cervical muscles; placebo needling group (n = 23) receiving conventional physical therapy and superficial dry needling at a point away from the trigger point. The primary outcome was the headache intensity and frequency. Neck disability, deep cervical flexor performance and range of motion were secondary outcomes. Outcomes were assessed immediately after treatment and one, three and six months later. RESULTS Sixty-five patients were finally included in the analysis. Headache intensity and neck disability decreased significantly more in the dry needling compared to sham and control groups after treatment and during all follow-ups. The frequency of headaches also reduced more in the dry needling than in control and sham groups, but it did not reach statistical significance. Higher cervical range of motion and enhancement of deep cervical flexors performance was also observed in the dry needling compared to sham and control groups. CONCLUSION Dry needling has a positive effect on pain and disability reduction, cervical range of motion and deep cervical flexor muscles performance in patients with cervicogenic headache and active trigger points, although the clinical relevance of the results was small.