Background The long non-coding RNA small nucleolar RNA host gene 16 (lncRNA SNHG6) is dysregulated in various malignant tumor. However, a definite conclusion on the clinical value of lncRNA SNHG6 expression in human cancers has not been determined. The purpose of the present meta-analysis was to comprehensively elucidate the association between SNHG6 expression and clinical outcomes in cancers. Methods A systematic search was performed through the PubMed, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wangfang databases for relevant studies. The pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were collected to estimate the prognostic value, and the odds ratios (ORs) with 95% CIs were used to evaluate the relationship between lncRNA SNHG6 expression and clinicopathological features, including tumor invasion depth, lymph node metastasis (LNM), distance metastasis (DM), and TNM stage. Results A total of 914 patients from 13 studies were included in this meta-analysis. The pooled results suggested that evaluated SNHG6 expression could predict an unfavorable overall survival (OS) (HR = 2.04, 95% CI:1.56~2.52) with no heterogeneity ( I 2 = 0.0%, p = 0.996). Subgroup analysis indicated a significant association between high SNHG6 expression and shorter OS in studies with digestive system cancers (HR = 2.05, 95%CI: 1.47-2.62), sample size < 70 (HR = 2.70, 95%CI: 1.29-4.11), and univariate and multivariate analysis (HR = 2.04, 95%CI: 1.44-2.64). Moreover, high SNHG6 expression was positively correlated with tumor invasion depth (OR = 1.76, 95%CI: 1.18-2.63), LNM (OR = 1.60, 95%CI: 1.18-2.17), DM (OR = 1.90, 95%CI: 1.37-2.64) and advanced TNM stage (OR = 1.88, 95%CI: 1.36-2.60) in patients with cancers. Conclusions High lncRNA SNHG6 expression was correlated with tumor invasion depth, LNM, DM, and advanced TNM stage, suggesting that SNHG6 may serve as a promising prognostic biomarker of human cancers.