Objective: To search new prognosis-related genes in gastric cancer by analyzing the high-throughput sequencing data of gastric cancer in TCGA database, and then provide data support for future studies. Methods: The RNA-seq expression matrix data and patient-related clinical data from 375 gastric cancer tissues and 45 adjacent noncancerous tissues were downloaded from the TCGA database. The data were collated and standardized based on the R language. The difference of gene expression was analyzed by the edgeR and DEseq software packages. The survival analysis of obtained differential genes was performed by the univariate and multivariate COX regressions combined with clinical data of patients, and then the genes with clinical significance were screened out. Results: A total of 364 differential genes were obtained by the edgeR and DEseq analysis. Subsequently, the functional enrichment analysis found that these genes were mainly involved in protein digestion and absorption, cytochrome P450 system of drug and exogenous substance metabolism, chemical carcinogenesis, gastric acid secretion and so on. The univariate COX regression analysis showed that FAP, FAT3, PDK4 and ZNF365 genes had significant influences on the prognosis of gastric cancer patients. The multivariate COX stepwise regression analysis showed that the risk model constructed by FAP and PDK4 could predict the prognosis of gastric cancer patients. Conclusion: FAP, FAT3, PDK4 and ZNF365 genes may be the prognostic markers of gastric cancer, which may provide data supports for future clinical and basic studies.