Background Botulinum neurotoxin A (BoNT-A) was the primary choice for preventive treatment of chronic migraine. Topiramate and acupuncture showed promising effect for the condition, but their effectiveness relative to BoNT-A was rarely studied. We aimed to perform a network meta-analysis to compare the effectiveness and acceptability between BoNT-A, topiramate, and acupuncture.Methods We searched OVID Medline, Embase, the Cochrane register of controlled trials (CENTRAL), the Chinese Clinical Trial Register, and clinicaltrials.gov for randomized controlled trials (RCTs) that compared BoNT-A, topiramate, and acupuncture with any of them or placebo in the preventive treatment of chronic migraine. Two independent reviewers screened RCTs, extracted data, and assessed risk of bias. A network meta-analysis was performed by using a frequentist approach and a random-effects model. The primary outcomes were reduction in monthly headache days and monthly migraine days at week 12. Acceptability was assessed by adverse event rate. The effect size of the primary outcomes was measured by using standard mean difference (SMD).Results We included 15 RCTs (n = 2545). Eleven RCTs were at low risk of bias. The network meta-analyses (n = 2061) showed that acupuncture (2061 participants; SMD − 1.61, 95%CI -2.35 to -0.87) and topiramate(582 participants; SMD − 0.4, 95%CI -0.75 to -0.04) ranked the most effective in the reduction of monthly headache days and migraine days, respectively; but they were not significantly superior over BoNT-A. Topiramate caused the most treatment-related adverse events and the highest rate of dropouts owing to adverse events.Conclusions Topiramate and acupuncture were not superior over BoNT-A. In terms of acceptability and accessibility of treatments, BoNT-A was still the primary choice for preventive treatment of chronic migraine.