CSF-1R, known as colony–stimulating factor receptor, is predominantly expressed in macrophages lineages such as monocytes and dendritic cells. It plays a crucial role in signal transduction, governing the differentiation, survival, proliferation, and migration of monocyte/macrophage lineage cells. Microglia, the principal macrophages in the brain, perform vital functions related to homeostasis and phagocytosis within the central nervous system. However, continuous activation of microglia can lead to neurodegenerative diseases by excessively producing inflammatory mediators. Recently, it is demonstrated that elimination of microglia through CSF-1R inhibition could reduce plaque formation in an Alzheimer’s disease in vivo model. Based on these sights, we tried to develop potent CSF-1R inhibitors as promising modulator of microglial activation. Herein, we report the evolution of novel CSF-1R inhibitors in the aspects of kinome selectivity, ADME properties including plasma and microsomal stability and BBB permeability. During our previous research on BRaf inhibitors, we found a methyl isoxazole scaffold, having CSF-1R inhibitory activity and designated it as lead compound. The lead, 5-methylisoxazole-4-carboxamide derivatives were evolved into 5-methylisoxazole-3-carboxamide derivatives to achieve better IC50 values and metabolic stability as well as BBB permeability. Most of the synthesized compounds showed favorable cellular activity and wide kinome selectivity as well as metabolic stability. Out of all the derivatives, especially N-(4-heterocycloalkyl-2-cycloalkylphenyl)-5-methylisoxazole-3-carboxamide, we identify highly selective and potent CSF1R inhibitor-7dri and it remarkably alleviated neuroinflammation in an in vivo LPS-induced model, establishing itself as a promising anti-neuroinflammatory agent.