Objective: Cervicogenic headache is a disabling headache where pharmacological management have limited effect. Thus, non-pharmacological management is warranted. Our objective was therefore to investigate the efficacy of chiropractic spinal manipulative therapy versus placebo (sham manipulation) and control (continued usual but non-manual management) for cervicogenic headache in a prospective 3-armed single-blinded, placebo, randomized controlled trial of 17 months' duration. Results: Nineteen participants were equally randomized into the three groups, and 12 participants completed the randomized controlled trial. Headache frequency improved at all time points in the chiropractic spinal manipulative therapy and the placebo group. Headache index improved in the chiropractic spinal manipulative therapy group at all time points, while it improved at 6 and 12 months' follow-up in the placebo group. The control group remained unchanged during the whole study period. Adverse events were few, mild and transient. Blinding was concealed throughout the RCT. Thus, our results suggest that manual-therapy might be a safe treatment option for participants with cervicogenic headache, but data need to be confirmed in a randomized controlled trial with sufficient sample size and statistical power. Trial registration ClinicalTrials.gov identifier: NCT01687881, 11 September 2012.