Proteases, such as tissue plasminogen activator, thrombin, metalloproteinases, and cathepsins, have complex functions in the mammalian brain under both normal and pathological conditions. Some of these proteases are expressed by neuronal cells, whereas others are made by the immunocompetent, macrophage-like cells of the brain: the microglia. This article reviews the physiological and pathological functions of these proteinases in the brain as well as recent findings linking extracellular proteases with neuronal cell death in ischemic or hemorrhagic stroke. Better understanding of protease expression and signaling, microglial activation, and their relationship with neuronal cell death during stroke injury could contribute to the development of relevant inhibitors as novel neuroprotective agents for treating ischemic stroke and intracerebral hemorrhage.