Bone marrow mesenchymal stem cells (MSCs) have the potential to be used in the cellular therapy of solid organs. However, tissue regeneration is limited by the death of transplanted cells. One of the main mechanisms of stem cell death in transplanted organs is through ischemia. In the present study, we sought to investigate whether a plant-derived antioxidant, berberine (BBR), could protect MSCs against MSCs apoptosis in a model of ischemia consisting of serum deprivation- and hypoxia-induced apoptosis in vitro. We also investigated the potential mechanism(s) that may mediate the action of berberine. We found that berberine significantly attenuated hypoxia-induced MSC apoptosis. Further study revealed that berberine could scavenger the reactive oxygen species (ROS), inhibit the c-jun NH(2)-terminal kinase (JNK), the loss of mitochondrial membrane potential and the release of cytochrome c (Cyt C) and caspase-3. In addition, we also showed that berberine could activate phosphoinositide-3 kinase (PI3K)/Akt and that pretreatment with PI3K/Akt inhibitors prevented berberine-induced inhibition of ROS, JNK and subsequent apoptosis, suggesting that the protective effects of berberine were PI3K/Akt-dependent. Taken together, these findings reveal that berberine protects against MSC apoptosis by preventing ROS-dependent and JNK-driven cell apoptosis in a PI3K/Akt-dependent manner. These data indicate that berberine is a promising anti-apoptotic agent for improving MSC survival during cell transplantation.