The design of novel targeted or combination therapies may improve treatment options for gastric cancer. In this study, we determined the inhibitory effects of 5-fluorouracil (5-FU) combined with gambogic acid (GA) on BGC-823 human gastric carcinoma cells in vitro and in vivo and investigated the underlying mechanisms. 5-FU combined with GA inhibited the viability of BGC-823 human gastric cells in a concentration-dependent manner. The pro-apoptotic activity of the two-drug combination was much stronger than single. Furthermore, the results showed GA could regulate the metabolic enzymes of 5-FU. GA decreased the mRNA levels of thymidine synthetase (TS) and dihydropyrimidine dehydrogenase (DPD), while increased the mRNA level of orotate phosphoribosyltransferase (OPRT). Moreover, combined treatment caused significantly growth inhibition of human tumor xenografts in vivo. Taken together, our data showed that GA attenuated 5-FU-induced apoptosis by modulating metabolic enzymes of 5-FU and the antigastric cancer effect of two drugs combination was much stronger than that of GA or 5-FU alone.