The concept of negative lymph node (NLN) counts has recently attracted attention as a prognostic indicator in various cancer. However, the correlation between NLN counts and patient prognosis in the setting of gastric cancer is not fully studied. Surveillance, Epidemiology, and End Results Program (SEER)-registered gastric cancer patients were used for analysis in this study. Clinicopathological characteristics, including race, age, gender, and tumor stage, grade, and cause specific survival were collected. Univariate and multivariate Cox proportional hazards model were used to assess the risk factors for survival. As results, X-tile plots identified 3 and 9 as the optimal cutoff value to divide the patients into high, middle and low risk subsets in terms of cause specific survival, and NLN was validated as independently prognostic factor in mulivariate Cox analysis (P < 0.001). Further analysis showed that NLN was a prognosis factor in each N stage. Collectively, our study results firmly demonstrated that the number of NLNs was an independent prognostic factor for gastric cancer patients, and together with the N stage, it could provide more accurate prognostic information than the N stage alone.