Microglia, a type of glial cells, are known to play critical roles in neurodegenerative diseases, and they respond to pathological conditions via microglial activation. The activation states, that are known to determine their functional roles, correlate closely with distinct migration patterns. For example, fully activated microglia with abnormally high motility and increased phagocytic behavior is an indication for neurodegenerative diseases. Since these cells are inherently exposed to diverse physicochemical stimulations in the microenvironment of the brain, a various physiological stimulations such as electrical, chemical, mechanical stimulations might be one of the key factors to regulate microglia activation. Therefore, this study aims to investigate the changes of microglial behavior under various physiological stimulations for therapeutic implications. To study the phenotypic difference of microglia as a response to external stimuli, the microfluidic platform was used for monitoring the effects of fluid shear stress and electric field (EF) on the migration and morphological change of cells in real time. In response to fluid shear stress, migrating behavior of microglia was significantly altered with pronounced increases in the speed of migration, the degree of scattering, and the alignment of trail pattern. In response to the applied EF, a number of microglia spontaneously exhibited phagocytic behavior for neighboring cells undergoing apoptosis. In addition, we have successfully developed an improved second microfluidic device, which can apply pulsatile electric field (EF) and parallel chemical gradient on cells that can mimic the chemical gradient of neurotoxic factors highly expressed in degenerative situation of brain. Our results imply the possibility of regulating the activation state of microglia by physical stimulations, which can provide new insights for pathological outbreaks of such diseases and may lead us to a novel therapeutic tool.