Background: Recent studies have demonstrated that the over-expression of Nanog contributes to the progression of various malignant tumors. However, the clinicopathological and prognostic role of Nanog in gastrointestinal luminal cancer remains controversial. Therefore, we conducted a meta-analysis to assess the role of Nanog in gastrointestinal luminal cancer. Methods: An electronic search for relevant literature was performed in PubMed, Cochrane Library, Web of Science, and EMBASE databases. The relationships between Nanog expression and clinicopathological features and survival outcomes were analyzed. Pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated by STATA14.2 and RevMan 5.3 software. Results: A total of 9 studies with 1526 patients were included in this meta-analysis. The positive expression of Nanog was related to gender, depth of infiltration, differentiation, and TNM stage; however, it was not associated with age, tumor size, or lymph node metastasis. Moreover, positive Nanog expression was correlated with a poor overall survival (OS) and poor disease-free survival (DFS) in gastrointestinal luminal cancer. Conclusion: The pooled results suggested that Nanog expression was associated with gender, depth of infiltration, differentiation, and TNM stage, and Nanog may be a potential biomarker to predict the prognosis of gastrointestinal luminal cancer.