The prognosis for gastric cancer is poor; therefore, there is urgent need for the development of novel, especially noninvasive surrogate biomarkers. NS5ATP9 is significantly overexpressed in gastric cancer tissues, and altered NS5ATP9 expression in human gastric cancer is associated with tumor recurrence. This study aimed to determine whether a correlation exists between NS5ATP9 mRNA levels in peripheral blood mononuclear cells (PBMCs) and gastric cancer prognosis in patients. NS5ATP9 mRNA levels were assessed by real-time RT-PCR in PBMC samples obtained from 207 gastric cancer patients, 47 patients with benign gastric lesions, and 78 healthy individuals. In addition, NS5ATP9 protein expression was evaluated by Western blot in PBMC samples from 30 gastric cancer patients and 30 healthy individuals, chosen randomly. Finally, clinicopathological data and survival of all gastric cancer patients were collected and analyzed. NS5ATP9 in PBMCs from gastric cancer patients was significantly upregulated both at mRNA and protein levels. Interestingly, NS5ATP9 mRNA overexpression in PBMCs was significantly associated with poor disease-free survival and overall survival of cancer patients, but not with tumor recurrence. Multivariate analysis showed NS5ATP9 mRNA levels and tumor lymph node metastasis were independent correlation with 3-year survival rate. Importantly, the diagnostic sensitivity and specificity (70.6 and 79.5 %, respectively) were higher for NS5ATP9 mRNA in PBMCs compared with the serum tumor markers CEA (45.0 and 84.6 %, respectively) and CA19-9 (61.5 and 69.2 %, respectively). These findings suggested that NS5ATP9 mRNA levels in PBMCs can be used for prognosis in gastric cancer patients.