The magnitude of the effect of fetuin-A and fetuin-B on non-alcoholic fatty liver disease (NAFLD) remains undefined. Therefore, the aim of this study was to synthesize previous findings to obtain a reliable estimation of this relationship. This study was registered in PROSPERO with the number CRD42019126314. Studies published not later than March 2019, examining the relationship between fetuin-A, fetuin-B, and NAFLD, were identified by a systematic search in the electronic databases of the Web of Science, PubMed, Embase, and Cochrane Library. Pooled estimates of standardized mean difference (SMD), calculated using the random-effects model in a meta-analysis, were applied to estimate the strength of the association between fetuin-A, fetuin-B, and NAFLD. Thirty publications were identified and analyzed based on specified inclusion criteria. Collectively, they consisted of 3800 NAFLD participants and 3614 controls. Compared with the controls, significant higher values of the fetuin-A (SMD = 0.83, 95% CI: 0.59 to 1.07, Z = 6.82, p < 0.001) and fetuin-B (SMD = 0.18, 95% CI: 0.02 to 0.33, Z = 2.27, p = 0.023) were observed in NAFLD patients. Meanwhile, in the subgroup analysis, the effect value of fetuin-A in the NASH group was significantly higher than that in the NAFL group (p = 0.036). The findings of this study suggest that elevated fetuin-A and fetuin-B may independently indicate the occurrence of NAFLD. Nevertheless, further research is needed to confirm these results.