Ischemia induces physiological alterations in neurons that lead to cell death. This study investigated the effects of pre-ischemic exercise on CA3 neurons. Rats were divided into three groups. Animals in the exercise group were trained 5 days a week for 4 weeks. Ischemia was induced by occlusion of both common carotid arteries (CCAs) for 20 min. Apoptotic cell death was detected by TUNEL assay. Furthermore, expression of different proteins was determined by immunohistochemical staining. The number of TUNEL-positive cells was significantly increased in the ischemia group, but pre-ischemic exercise significantly reduced apoptotic cell death (P < 0.001). In addition, our results showed a significant increase in the Bax/Bcl-2 ratio in the ischemia group. Pre-ischemic exercise attenuated this ratio (P < 0.05). Furthermore, the number of active caspase-3-positive neurons was significantly increased in the ischemia group, which was reduced markedly by exercise preconditioning (P < 0.05). This study showed that pre-ischemic exercise can exert neuroprotective effects against ischemia in CA3 neurons.