Protoapigenone, a natural derivative of the flavonoid apigenin, has been shown to exhibit potent antitumor activity in vitro and in vivo; the precise mechanism of action, however, is not fully elucidated. In this study, we investigated and compared the mechanisms by which protoapigenone and apigenin caused cell death in the human breast cancer MDA-MB-231 cells. Flow cytometry analysis revealed that protoapigenone induced apoptosis with 10-fold greater potency than apigenin. Cancer cells treated with protoapigenone resulted in persistent activation of mitogen-activated protein kinase (MAPK) ERK, JNK, and p38, hyperphosphorylation of Bcl-2 and Bcl-xL, and loss of mitochondrial membrane potential (MMP). The MAPK inhibitors effectively prevented the loss of MMP and apoptosis induced by protoapigenone. Treatment of cells with protoapigenone led to increased levels of reactive oxygen species (ROS) and decreased levels of intracellular glutathione. The thiol-antioxidant N-acetylcysteine abolished protoapigenone-induced MAPK activation, mitochondrial dysfunction, and apoptosis. These results suggest that the induction of oxidative stress preceding the activation of MAPK is required to initiate the mitochondria-mediated apoptosis induced by protoapigenone. Additionally, protoapigenone-induced JNK activation was linked to thiol modification of glutathione S-transferase π (GSTpi), which impeded GSTpi inhibition of JNK. In contrast to protoapigenone, apigenin-induced apoptosis was neither dependent on ROS nor on MAPK. Structure-activity relationship studies suggested that the thiol reacting effect of protoapigenone might be associated with an α, β-unsaturated ketone moiety in the structure of ring B.