Background: Migraine surgery at 1 of 6 identified “trigger sites” of a target cranial sensory nerve has rapidly grown in popularity since 2000. This study summarizes the effect of migraine surgery on headache severity, headache frequency, and the migraine headache index score which is derived by multiplying migraine severity, frequency, and duration. Materials and Methods: This is a PRISMA-compliant systematic review of 5 databases searched from inception through May 2020 and is registered under the PROSPERO ID: CRD42020197085. Clinical trials treating headaches with surgery were included. Risk of bias was assessed in randomized controlled trials. Meta-analyses were performed on outcomes using a random effects model to determine the pooled mean change from baseline and when possible, to compare treatment to control. Results: 18 studies met criteria including 6 randomized controlled trials, 1 controlled clinical trial, and 11 uncontrolled clinical trials treated 1143 patients with pathologies including migraine, occipital migraine, frontal migraine, occipital nerve triggered headache, frontal headache, occipital neuralgia, and cervicogenic headache. Migraine surgery reduced headache frequency at 1 year postoperative by 13.0 days per month as compared to baseline ( I2 = 0%), reduced headache severity at 8 weeks to 5 years postoperative by 4.16 points on a 0 to 10 scale as compared to baseline ( I2 = 53%), and reduced migraine headache index at 1 to 5 years postoperative by 83.1 points as compared to baseline ( I2 = 2%). These meta-analyses are limited by a small number of studies that could be analyzed, including studies with high risk of bias. Conclusion: Migraine surgery provided a clinically and statistically significant reduction in headache frequency, severity, and migraine headache index scores. Additional studies, including randomized controlled trials with low risk-of-bias should be performed to improve the precision of the outcome improvements.