Background: Abnormal regulation of genes was closely related to gastric cancer. The characterization of gastric cancer has necessitated the development of new therapeutics as well as the identification of prognostic markers to predict the response to novel drugs. Methods: In our study, we have performed RNA sequencing analysis on gastric cancer tissues that decreased levels of RNF43 and PWWP2B were significantly associated with recurrence. RNF43 inhibit gastric cancer-related Wnt/β-catenin signaling by interacting with Wnt receptors. PWWP2B is unknown gene which is downregulated in gastric cancer. Therefore, we investigated the screening of 1,449 FDA-approved drugs in male-derived human cell lines such as HAP1, HAP1 RNF43 KO, and HAP1 PWWP2B KO and female-derived human cell line such as SNU620 cells. Results: We demonstrated that RNF43 KO and PWWP2B KO cells showed significantly increased proliferation and migration abilities. Next, we investigated the inhibitory effects of 1,449 drugs in HAP1, HAP1 RNF43 KO, HAP1 PWWP2B KO, and SNU620 cells. After the first round of screening, candidate drugs were selected based on an inhibition rate of > 60% loss of viability compared to wild type cells. Among these FDA-approved drugs, nine drugs (aprepitant, docetaxel trihydrate, ethinyl estradiol, griseofulvin, INC280, pelitinib, pimobendan, tepotinib, and uprosertib) showed strong inhibitory effects in RNF43 KO cells and PWWP2B KO cells. Migration and apoptosis analyses demonstrated that docetaxel trihydrate and pelitinib showed the best inhibition and apoptotic rates, with the smallest half maximal inhibitory concentrations among the screened candidate drugs. In a murine xenograft model, tumor volumes were significantly reduced in the docetaxel trihydrate, uprosertib or pelitinib-treated group, when administered by oral gavage.Conclusions: Our data demonstrated that RNF43 and PWWP2B are a biomarker that predict recurrence of gastric cancer. Our findings suggest that pelitinib could be used as novel therapeutic agents for the prevention and treatment of gastric cancer with an aberrant decrease in RNF43 and PWWP2B expression.