Objectives To investigate long‐term outcomes in per‐protocol chronic cluster headache patients (n = 7), 18 and 24 months after participation in “Pilot study of sphenopalatine injection of onabotulinumtoxinA for the treatment of intractable chronic cluster headache.” Methods Data were collected prospectively through headache diaries, HIT‐6, and open questionnaire forms at 18 and 24 months after the first treatment. Patients had access to repeated injections when needed. Results An overall significant reduction in cluster headache attack frequency per month (57.3 ± 35.6 at baseline vs 12.4 ± 15.2 at month 18 and 24.6 ± 19.2 at month 24) was found. In addition, there was a reduction in attacks with severe and unbearably intensity (50.0 ± 38.3 at baseline vs 10.1 ± 14.7 at month 18 and 16.6 ± 13.7 at month 24) and an increase in attack free days (4.2 ± 5.9 at baseline vs 19.1 ± 9.4 at month 18 and 12.9 ± 8.8 at month 24). Conclusions Our findings suggest sustained headache relief after repeated onabotulinumtoxinA injections toward the sphenopalatine ganglion in intractable chronic cluster headache. A placebo‐controlled trial with long‐term follow‐up is warranted.