Microglia constitutes the first line of defense against infection and injury in the brain. We previously demonstrated that activated microglia express the Foxp3 gene. However, the role of Foxp3 in cells other than Treg is generally unknown. Therefore, this study was conducted to determine the effects of Foxp3 in LPS-induced activation of microglial cells. The effects of Foxp3 on gene expression profiles in activated microglial cells were evaluated by microarray analysis, which revealed that the Warburg effect, cytokine-cytokine receptor interaction, immune and inflammatory response, Jak-STAT signaling pathway, MAPK signaling pathway, cell adhesion molecules, p53 signaling pathway, and Wnt signaling pathway-related genes were up-regulated in LPS-treated Foxp3-deficient microglial cells. These findings indicate that Foxp3 might regulate the Warburg effect and inflammatory response in activated microglial cells.