Background and purpose Onabotulinumtoxin A was effective and well tolerated for prophylaxis of headache in patients with chronic migraine ( CM ) in two randomized, double‐blind, placebo‐controlled, phase 3 trials. To further assess the safety and tolerability of onabotulinumtoxin A in CM prophylaxis in adults, the pooled safety data from four double‐blind, placebo‐controlled trials were analyzed. Methods The pooled analysis included two phase 2 and two phase 3 double‐blind, placebo‐controlled trials. The safety population was 2436 patients, 1997 of whom received ≥1 dose of onabotulinumtoxinA. The studies shared similar dosing intervals (approximately 12 weeks) with doses between 75 and 260 U. Safety assessments included adverse events ( AE s), physical examination and clinical laboratory tests. Results Onabotulinumtoxin A was safe and well tolerated, with a low discontinuation rate (3.4%) due to AE s. The majority of patients in this pooled analysis received doses between 150 and 200 U, with an average of 163 U per treatment cycle. Of the 1997 patients who received any onabotulinumtoxin A injections, 1455 patients (72.9%) reported at least one AE . Neck pain (12.6%) was the most common onabotulinumtoxin A ‐associated AE , followed by muscle weakness (8.0%), musculoskeletal stiffness (6.1%) and eyelid ptosis (4.6%). Serious AE s were infrequent, occurring in 5.4% of patients who received any onabotulinumtoxin A treatment and 3.0% of patients receiving placebo. AE s were consistent with the known tolerability profile of onabotulinumtoxin A . Conclusions Multiple treatments with onabotulinumtoxinA at doses of 75–260 U administered every 12 weeks, and up to five treatment cycles, were well tolerated for the prophylaxis of headache in adults with CM .