The principle of magnetic hyperthermia is to generate localized heating on target proteins, cells and tissue that are targeted by magnetic nanoparticles (MNPs) upon stimulation by remotely applied high frequency alternating magnetic field (AMF). Beyond its traditional applications in hyperthermia therapy, recent studies demonstrated the feasibility of magnetic hyperthermia as a new strategy for neural stimulation. The objective of this study is to examine the feasibility of localized magnetic hyperthermia (i.e. MNP/AMF hyperthermia) as a new strategy for brain stimulation, especially in modulating microglia activity and behaviors in vivo. This was examined by correlating a varying degree of MNP/AMF-induced thermal dose with the extent of microglial activation in the mouse brain. The MNP/AMF hyperthermia stimulation applied at a mild thermal dose to the mouse hippocampus significantly increased the infiltration of microglia and altered their morphology towards reactive and ameboid-like phenotypes in a thermal dose-dependent manner. Importantly, these responses were associated with increased expression of heat shock protein 70 (HSP70), a molecular chaperon protein, and LC3II, a marker of autophagic activity. Our findings support the feasibility of developing mild magnetic hyperthermia as a new strategy for localized stimulation of brain tissue.