ATG9A is an integral membrane protein required for autophagosome formation and a membrane carrier in the autophagy pathways. The present study was designed to investigate the expression of ATG9A in oral squamous cell carcinoma (OSCC). Clinically annotated tumor specimens from 90 patients with OSCC were subjected to immunohistochemistry using an antibody against ATG9A and immunoreactivity was scored using an immunoreactivity score (IRS). Scores were compared with clinical and pathologic data to assess association with outcome. Overexpression of ATG9A was defined as an IRS of ≥9 by receiver operating characteristics curve analysis and was identified in 25 (28 %) of 90 cases. ATG9A overexpression was associated with disease recurrence and overall survival (OS) in both univariate (p = 0.030 and 0.025, respectively) and multivariate (p = 0.026 and 0.038, respectively) Cox analyses. Kaplan-Meier plots also showed that patients with ATG9A overexpression had shorter 3-year OS (p = 0.017) and time to recurrence (p = 0.021) than those with low ATG9A expression. These results suggest that the presence of ATG9A in the cytoplasm of tumor cells may be an independent biomarker for disease recurrence and survival in patients with OSCC.