Cochinchina momordica seed is the dried ripe seed of Momordica cochinchinensis (Lour.) Spreng, which is a kind of fruit and consumed for dietary as well as medicinal uses. In this study, using the human SGC7901 and MKN-28 gastric cancer cell lines, we explored the anticancer activity of the extract from cochinchina momordica seed (ECMS). ECMS inhibited significantly the survival rates of SGC7901 and MKN-28 cells in concentration- and time-dependent manners by MTT assay. The typical apoptotic morphological changes were observed by Hoechst 33258 dye assay after SGC7901 and MKN-28 cells were treated with ECMS for 48 h. Flow cytometry analysis revealed that ECMS-treatment blocked the cells at the S phase of cell cycle. Furthermore, the protein expression levels of poly (ADP-ribose) polymerase (PARP) and Bcl-2 were downregulated notably by ECMS-treatment, whereas those of Fas/Fas-associated death domain, p53, and Bax were upregulated in SGC7901 cells. ECMS dramatically enhanced the enzymatic activities of caspase-3 and caspase-9 whilst slightly increased caspase-8 activity. Taken together, this study demonstrated that ECMS exerted cytotoxic activities via PARP and p53 signal pathways in the human gastric cancer cells.