We attempted to explore the prevalence of HBV and HCV infections in patients with systemic lupus erythematous (SLE) via a systematic review. Articles published before June 2017 and, related to prevalence rates for HBV and HCV infection in SLE patient were identified in PubMed, Embase, CNKI, and Wanfang databases. Based on these searches 22 studies were selected for further analysis. The OR of HBsAg positive rate in SLE patients compared with control population was 0.28, with significant heterogeneity identified among the studies (I2 = 92%, P < 0.00001). Following exclusion of one study, the adjusted OR of HBsAg in patients with SLE was 0.24, and no significant heterogeneity was observed (I2 = 32%, P = 0.15). The adjusted OR of HBcAb positive rate in SLE patients compared with control population was 0.40, with no significant heterogeneity between studies (I2 = 0%, P = 0.56). The risk of having HCV infection by SLE patients was higher compared with the control subjects (OR = 2.91). In conclusion, this meta-analysis suggested that SLE might exert a role of protection against HBV but not for HCV infection. Further epidemiological and experimental studies are necessary to explore the role and mechanisms by which SLE affects HBV/HCV infections.