Background: Primary insomnia is a widespread and refractory disease. Moxibustion therapy for insomnia shows some advantages compared with conventional therapies. This systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted to evaluate the effectiveness and safety of moxibustion therapy for insomnia. Methods: We conducted a comprehensive literature review of the CENTRAL, PubMed, EMBASE, Web of science, CNKI, VIP, and Wanfang Data databases from their inception to July 2015 for RCTs that compared moxibustion with western medications, oral Chinese medicine, or other methods of traditional Chinese medicine (TCM) in patients with primary insomnia. The primary outcome measure was effective rate and secondary outcome measure was adverse events. Data collection and analysis included risk of bias evaluation, meta-analysis, sensitivity analysis, publication bias and adverse events analysis according to corresponding criteria. Results: The study included 22 RCTs (1,971 patients). The quality of the studies was low. The overall meta-analysis demonstrated that moxibustion was more effective for insomnia than western medications, oral Chinese medicine and other TCM therapies (RR = 1.17, 95 % CI 1.12 to 1.23, P < 0.00001). Subgroup analyses demonstrated that moxibustion was more effective for insomnia than western medications (RR = 1.16, 95 % CI 1.09 to 1.24, P < 0.00001), oral Chinese medicine (RR = 1.11, 95 % CI 1.04 to 1.18, P = 0.002), and other TCM therapies (RR = 1.22, 95 % CI 1.15 to 1.30, P < 0. 00001). There were no serious adverse effects associated with moxibustion therapy for insomnia, and the rate of adverse events was low. Conclusion: It is difficult to get the conclusion regarding the effectiveness and safety of moxibustion for primary insomnia due to insufficient evidence, such as the high risk of bias in the included studies, small sample sizes, and few reports on adverse effects. Moxibustion should be considered as a novel therapeutic option for insomnia, and more rigorous clinical trials of moxibustion therapy for insomnia are needed to assess its effects.