Because of its high nutritional value and anti-cancer features, Momordica charantia has gained a lot of interest as a supplementary medicine in recent years. This study reveals the possible underlying mechanism of action of Momordica charantia seed extract (McSE), which was shown to suppress the migration and proliferation of MCF-7 cells. McSE blocked cell growth and 17-β-Estradiol (E2)-induced cell migration with an IC50 value of 242.2 μg/mL. The non-genomic signaling kinases ERK1/2 and PI3K/AKT were increased by a short time (15 min) administration of E2 (1nM) at low concentration, which led to the activation of caspase-9. Treatment with McSE significantly reduced the activation of ERK1/2 and PI3K/AKT and the phosphorylation of caspase-9. Based on the findings of the migration assay it is shown that McSE administration inhibited cell migration and significantly reduced the relative closure of scratches. Our study suggests, for the first time, that McSE has the ability to inhibit breast cancer cell growth by suppressing non-genomic estrogen receptor signaling kinases and caspase-9 phosphorylation.