Chronic stress causes emotional disturbances and is a risk factor for mental illnesses such as depression. It was reported that chronic social stress activates microglia in the medial prefrontal cortex (mPFC) through innate immune receptors TLR2/4, leading to depressive-like behavior. Since lipopolysaccharide, a TLR4 ligand, differently activates microglia isolated from left and right hemispheres, we analyzed chronic social stress-induced gene expression changes in mPFC microglia of each hemisphere using laser microdissection microscopy combined with RNA-seq. Given individual variability in stress susceptibility, we categorized the stressed mice into susceptible and resilient mice based on the level of social avoidance. We identified genes that increased or decreased in expression in mPFC microglia with chronic stress. Many of these genes responded to stress differently between left and right hemispheres and between susceptible and resilient mice. Notably, the genes altered in expression only in resilient mice showed hemispheric asymmetry in their stress responses. These findings demonstrate hemispheric asymmetry of chronic stress-induced microglial responses and suggest its relevance to stress resilience.