Microglial cells are the resident immune cells of the Central Nervous System (CNS). Under physiological conditions, microglia constantly surveil their surrounding parenchyma and act as scavenger cells to maintain a healthy environment within the CNS. Following different insults to the CNS, microglia turn into a “reactive” state characterized by the production of inflammatory mediators that promote tissue repair to restore homeostasis. If inflammation is not in check, chronic microglia activation results in damage to the brain and leads to persistent cognitive impairments. Microglia display sex-specific features in adult mice; specifically, microglia from female mice have been found to be less reactive. Exposure to space radiation results in chronic activation of microglia in male but not in female mice. Interestingly, manipulating microglia after exposure to space radiation can prevent the development of cognitive deficits in adult male mice. These discoveries may provide clues in how to protect astronauts’ cognitive functions both during the missions and after return.