Gastric cancer (GC) is one of the most common malignant cancers worldwide. However, little is known about the molecular process underlying this disease and its progression. This study investigated correlations between the expression of a mitochondrial inner membrane protein translocase of inner mitochondrial membrane 9 homolog (TIMM9) and various clinicopathologic parameters as well as patients' survival. Methods: Gastric tissue samples were obtained from 140 patients with GC and expression levels of TIMM9 were analyzed through immunohistochemistry. Paired t tests were used to analyze the differences in the expression levels of TIMM9 in both tumor and nontumor tissues for each patient. Two-tailed χ2 tests were performed to determine whether the differences in TIMM9 expression and clinicopathologic parameters were significant. Time-to-event endpoints for clinicopathologic parameters were plotted using the Kaplan–Meier method, and statistical significance was determined using univariate log-rank tests. Cox proportional hazard model was used for multivariate analysis to determine the independence of prognostic effects of TIMM9 expression. Results: A borderline association was found between overexpression of TIMM9 and vascular invasion (p = 0.0887). Patients with high expression levels of TIMM9 achieved a significantly lower disease-free survival rate compared with those with low expression levels (p = 0.005). Multivariate Cox regression analysis showed that overexpression of TIMM9 was an independent prognostic marker for GC (p = 0.011). Conclusion: Overexpression of TIMM9 can be used as a marker to predict the outcome of patients with GC.