Numerous studies show the neuroprotective effects of estrogen, but the underlying mechanism still remains unclear. Recent studies indicate that mitochondria are critically involved in estrogen-mediated neuroprotection. Mitochondria are the main sources of cellular energy and reactive oxygen species (ROS), they play an important role in signaling transduction and cellular life-death decisions. Estrogen exerts multiple effects on mitochondria under physiological and/or pathological conditions, these effects may include modulating ATP and ROS production, preserving mitochondria membrane potential, maintaining calcium homeostasis, and regulating mitochondrial gene and protein expression, etc. In this paper, we discussed the neuroprotective effects of estrogen, particularly focused on the underlying mechanisms related to mitochondria.