5-Fluorouracil (5-Fu) is one of the most commonly used drugs to treat gastric cancer; however, drug-resistance in cancer cells reduces the efficacy of 5-Fu. Celecoxib may be able to reduce resistance to 5-Fu chemotherapy. The aim of the present study was to investigate the inhibitory effects of a combination of 5-Fu and celecoxib on implanted gastric cancer xenografts in nude mice and to elucidate the underlying mechanism. A tumor-bearing nude mice model was established. The mice were divided into blank control, 5-Fu, celecoxib and combination groups. The weight change and the tumor inhibition rate in each group were calculated. Immunocytochemistry, reverse transcription-polymerase chain reaction and western blotting methods were used to observe hypoxia-inducible factor-2α (HIF-2α), ATP-binding cassette transporter G2 (ABCG2) and octamer-binding transcription factor 4 (Oct-4) expression in the SGC7901 cells. Inhibition of the growth of the implanted gastric cancer was observed in the 5-Fu, celecoxib and combination groups. In the celecoxib and combination treatment groups, the mean tumor mass was significantly less than that in the control group (P<0.05), and the mean tumor mass in the combination treatment group was significantly less than that in the 5-Fu group (P<0.05). The tumor inhibition rates in the 5-Fu, celecoxib and combination groups were 26.36, 59.70 and 88.37%, respectively. The combination group exhibited the highest inhibition rate; the inhibition rates of the combination and celecoxib groups were significantly higher compared with the 5-Fu group (P<0.05). The expression levels of HIF-2, ABCG2 and Oct-4 mRNA and protein were high in the blank control group, and were further increased in the 5-Fu group. However, in the celecoxib and combination groups, the expression levels were lower compared with those in the control group. Significant differences were identified among the 5-Fu, celecoxib and combination groups (P<0.01). Celecoxib has antitumor effects in vivo. The mechanism may be associated with the reduced expression of cancer stem cell markers HIF-2α, Oct-4 and ABCG2. 5-Fu and celecoxib have a synergistic antitumor effect. The mechanism associated with the amelioration of resistance to chemotherapy in gastric cancer and the enhancement of the effect of chemotherapy may be via the reduction of the expression of HIF-2α, ABCG2, Oct-4 and other cancer stem cell markers in the tumor tissues.