MicroRNAs (miRNAs) are small, non-protein-coding RNAs that function as tumour suppressors or oncogenes. A single nucleotide change in the sequence of pre-miRNA can affect miRNA expression, so single-nucleotide polymorphisms (SNPs) in pre-miRNA may be biomarkers for biomedical applications. In this study, we performed a genetic association study between the SNP (rs11614913) in pre-miRNA-196a and esophageal squamous cell carcinoma (ESCC) susceptibility in a case-control study. We found that the homozygote CC of this SNP increased the risk of ESCC compared with the homozygote TT and the risk was more evident among smokers than non-smokers. Therefore, this functional SNP may be a biomarker for ESCC outcome.