The survival rate of esophageal squamous cell cancer (ESCC) patients is still dismal. Therefore, novel prognostic biomarkers are critically needed for patients with ESCC. SLC9A9 has been reported to be downregulated in hormone-sensitive prostate cancer; however, the correlations between SLC9A9 and ESCC prognosis are unclear. The aim of this study is to evaluate the expression and prognostic significance of SLC9A9 in resectable ESCC. Fresh frozen or paraffin-embedded samples were collected from 167 or 59 patients with resectable ESCC, respectively. The expression of SLC9A9 was assessed by reverse transcription and quantitative real-time polymerase chain reaction analysis (167 patients) and immunohistochemistry (61 patients). The expression of SLC9A9 was not associated with patient clinicopathological characteristics at both transcription and protein levels. The 5-year overall survival in the high SLC9A9 messenger RNA (mRNA) group (n = 106) was poorer than that in the low expression group (n = 61) (34.6 vs. 65.9 %, P < 0.001). Notably, higher SLC9A9 protein expression was also correlated with lower 5-year overall survival (33.1 vs. 66.5 %, P = 0.023). Moreover, multivariate analysis revealed that SLC9A9 mRNA (HR, 2.41; 95 % CI, 1.47–3.97; P = 0.001) and protein (HR, 2.31; 95 %CI, 1.06–5.02; P = 0.034) were independent prognostic factors. In conclusion, the expression of SLC9A9 can be a prognostic predictor for ESCC.