Microglia are the principle immune cells of the brain. Once activated, microglial cells may exhibit a wide repertoire of the context-dependent profiles ranging from highly neurotoxic to more protective and pro-regenerative cellular phenotypes. While to date the mechanisms involved in the molecular regulation of the microglia polarization phenotypes remain elusive, growing evidence suggests that gender may markedly affect the inflammatory and/or glial responses following brain injuries. In the recent years, special attention has been given to the role of microglia in sexual dimorphism, both in healthy brain and diseased brain. Here, we review recent advances revealing microglia as an important determinant of gender differences under physiological conditions and in injured brain. We also discuss how microglia-driven innate immunity and signaling pathways might be involved in the sex-dependent responses following brain ischemic injury. Finally we describe how advanced methods such as live imaging techniques may help elucidate the role of microglia in the modulation of immune responses and gender difference after stroke.