The present study assessed the clinical efficacy of radiofrequency cervical zygapophyseal joint neurotomy in patients with cervicogenic headache. Fifteen consecutive patients with cervicogenic headache were treated and then assessed one week prior to treatment and, at short-term (8 weeks), intermediate (mean 8.8 months) and long-term (mean 16.8 months) follow-ups. The following were taken as outcome parameters: Visual Analogue Scale (VAS), 7-point Verbal Rating Scale (VRS), number of headache days per week and analgesic intake per week. The results of this study showed that radiofrequency neurotomy of the cervical zygapophyseal joints significantly reduced headache severity in 12 (80%) patients, both at short-term and long-term follow-up assessed by 7-point VRS. Mean VAS decrease was 31.4 mm (p < 0.001) and 53.5 mm (p < 0.0001) respectively in this period. The average mean number of headache days per week decreased from 5.8 days to 2.8 days (p = 0.001) and the average analgesic intake per week showed a reduction from a mean of 17.5 tablets to a mean of 3.4 tablets (p = 0.003). A definitive conclusion about the clinical efficacy of this treatment can only be drawn from a randomized controlled trial.