Background and aims: Recently, studies indicate that Nanog is over-expressed in hepatocellular carcinoma (HCC); however, the relationship between Nanog expression and clinicopathological and prognostic value remains controversial. Therefore, we conducted a meta-analysis to explore the role of Nanog in HCC. Methods: Articles were included from PubMed, Cochrane Library, Web of Science, EMBASE database, Chinese CNKI, and the Chinese WanFang database. The relationships between Nanog expression, clinicopathological features, and survival rate were calculated. Pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated with STATA14.2. Results: A total of 845 patients from 9 articles were enrolled. Positive Nanog expression was correlated with HBsAg, differentiation, and TNM stage, although it was not related to gender, age, alpha-fetoprotein (AFP), tumor size, tumor number, liver cirrhosis, and vascular invasion. Positive Nanog expression indicates a poor 3-year and 5-year overall survival and disease-free survival rate. Conclusion: The results show that Nanog expression was related to HBsAg, differentiation, and TNM stage in HCC. Nanog may be an unfavorable prognostic biomarker for HCC.