Neuroprotection by estrogen in the CNS is well-documented and comprises the intricate regulation of cell-cell communication between neurons and supportive non-neuronal glial cells. It is assumed that these interactions are essential for cell survival under pathological and toxic conditions by regulating the allocation of trophic molecules, e.g., growth factors, controlling relevant intracellular anti-apoptotic and death cascades, and attenuating inflammatory processes. Malfunction and disturbance of mitochondria are doubtlessly associated with brain cell degeneration during neurotoxic and neurodegenerative processes. Estrogen has been documented as protective agent in the brain by stimulating growth factor supply and cell-intrinsic pro-/anti-apoptotic signaling pathways. In recent years, an additional estrogen-dependent safe-guarding strategy comes into the focus of neuronal protection. The mitochondrial compartment appears to be regulated by estrogen at the level of ATP and reactive oxygen species production as well as under a structural-functional viewpoint. In the present article, we would like to highlight recent data which demonstrate that sex steroids can directly and indirectly interfere with mitochondrial properties via non-nuclear, presumably mitochondria-intrinsic and nuclear signaling mechanisms. This enables mitochondria to cope with pathological processes and provide stabile local energy homeostasis and an anti-apoptotic base setting in the brain which, in turn, is a prerequisite for neuronal survival.