A novel technique for injection of OnabotulinumtoxinA (BTA) towards the sphenopalatine ganglion (SPG) has shown promise in refractory chronic migraine (CM) and chronic cluster headache (CCH). Open label safety and efficacy data are presented here. Patients with refractory CM or CCH who had received at least one injection and completed headache diaries were included. Efficacy was defined as ≥50% reduction in moderate-to-severe headache days for CM, or ≥50% reduction in attack frequency for CCH, at weeks five to eight. Over 261 injections, there were 123 adverse events (AE), of which one was serious. Most (93%) AEs were mild and all were transient. The 50% response to one injection was 81% for CM and 69% for CCH. The response gradually reduced over subsequent months for CM but stayed between 55% and 67% for CCH. Repeated injections were beneficial. Injections resulted in improvement for both groups and was maintained with repeated injections. Repeat injection after three months may be beneficial in CM. Adverse events were not uncommon, but universally transient, presumably as a result of the mechanism of action of BTA. Repeated BTA injection towards the SPG could be an effective treatment for refractory CM and CCH. Larger, randomised, placebo-controlled trials are required.