Some studies have reported that hepatitis B virus (HBV) infection affects the risk of nonalcoholic fatty liver disease (NAFLD). However, this association is controversial. We conducted a systematic review and meta-analysis to investigate the relationship between HBV infection and NAFLD. Relevant studies published before May 2017 were identified by searching PubMed, EMBASE, and ISI Web of Science. We used the random-effects model proposed by DerSimonian and Laird to quantify the relationship between HBV infection and risk of NAFLD. We also conducted subgroup and sensitivity analyses to validate the stability of the results. Five articles, comprising 8,272 HBV-infected patients and 111,631 uninfected controls, were included in our research. Our meta-analysis suggested that the risk of NAFLD was significantly lower in HBV-infected patients than in uninfected controls, with heterogeneity between studies (summary odds ratio [OR] = 0.71; confidence interval [CI] = 0.53–0.90; I² = 75.2%). However, the inverse relationship was observed in only cohort (OR = 0.83; 95% CI = 0.73–0.94) and cross-sectional studies (OR = 0.63; 95% CI = 0.47–0.79), not case-control studies (OR = 3.96; 95% CI = 2.10–7.48). In conclusion, HBV infection was inversely associated with the risk of NAFLD.