An A/G polymorphism (rs3746444) has been identified in the miR-499 gene that can change the conformation of the secondary gene structure and thereby directly affect binding to target mRNAs and the microRNA (miRNA) maturation process, thus altering protein expression and potentially contributing to cancer susceptibility. Numerous studies investigating the association between the rs3746444 polymorphism and cancers have been published; however, results are inconsistent and inconclusive. To clarify the relationship between the miR-499 rs3746444 polymorphism and cancer, we conducted a comprehensive meta-analysis on 14 case-control studies comprising 7189 cases and 8577 controls. Odds ratios (OR) and 95% confidence intervals (CI) were calculated by using dominant, recessive, and co-dominant genetic models. A publication bias test and subgroup analysis were also performed. Results showed that the G allele was associated with a significantly increased cancer risk compared to the A allele (OR = 1.09; 95% CI = 1.00-1.18). Similarly, moderately elevated risks were also observed in overall analyses in the dominant model (OR = 1.13; 95% CI = 1.01-1.26). Moreover, significantly increased risks were observed in Asian populations (G allele vs A allele: OR = 1.18; 95% CI = 1.01-1.37; GG vs AA: OR = 1.36; 95% CI = 1.07-1.73; dominant model: OR = 1.19; 95% CI = 1.00-1.41; recessive model: OR = 1.31; 95% CI = 1.03-1.66), but not in European populations. These findings indicate that the miR-499 rs3746444 polymorphism is associated with an increased cancer risk.