Evodiae Fructus is the dried unripe fruit of Evodia rutaecarpa, and has traditionally been used for treating stomachache and diarrhea. Evodiamine and rutaecarpine, the major biologically active compounds of Evodiae Fructus, are reported to have anti-oxidative and anti-inflammatory effects, as well as inhibit proliferation and metastasis of various cancer cells. The current study investigates the anti-oxidative and anti-cancer effects of the Evodiae Fructus extract, considering varying concentrations of methanol extraction (40, 80, and 95%). High contents of total phenolic compounds were determined in the order of extracts 80, 95, and 40%. Evaluating contents of the 95, 80, and 40% extracts revealed 36.77, 7.29, and 1.86 μg/mg evodiamine, respectively, and 53.02, 17.16, and 3.79 μg/mg rutaecarpine, respectively, with the highest content of both compounds obtained in the 95% extract. DPPH radical scavenging activity was observed to be inversely proportional to the contents of total phenolic compounds, with decreasing SC50 values obtained in the order 80, 95, and 40% extract. The 95 and 80% extracts exerted toxicity to AGS gastric cancer cells, but the 40% extract was non-toxic. Evodiamine is a known anti-cancer agent, and could be responsible for the observed toxicity. Cleavage of PARP, and Caspase-3, -7, -8 and -9 was observed in the 95% extract-treated AGS cells, indicating that cell toxicity exerted by the 95% extract could be attributed to apoptosis.