Chronic neuroinflammation with sustained microglial activation occurs following moderate-to-severe traumatic brain injury (TBI) and is believed to contribute to subsequent neurodegeneration and neurological deficits. Microglia, the primary innate immune cells in brain, are dependent on colony stimulating factor 1 receptor (CSF1R) signaling for their survival. In this translational study, we examined the effects of delayed depletion and subsequent repopulation of microglia on chronic neurodegeneration and functional recovery up to three months posttrauma. A CSF1R inhibitor, PLX5622, was administered to injured adult male C57Bl/6 mice at one month after controlled cortical impact to remove chronically activated microglia, and the inihibitor was withdrawn 1 week later to allow microglial repopulation. Following TBI, the repopulated microglia displayed a ramified morphology, similar to that of sham control uninjured animals, whereas microglia in untreated injured animals showed the typical chronic posttraumatic hypertrophic morphology. PLX5622 treatment limited TBIassociated neuropathological changes at 3 months posttrauma; these included a smaller cortical lesion, reduced neuronal cell death in the injured cortex and ipsilateral hippocampus, and decreased NOX2-dependent reactive microgliosis. Furthermore, delayed depletion of microglia led to widespread changes in the cortical transcriptome, including alterations in gene pathways involved in neuroinflammation, oxidative stress, and neuroplasticity.PLX5622 treated animals showed significantly improved neurological recovery using a variety of complementary neurobehavioral evaluations.These included beam walk and rotorod tests for sensori-motor function, as well as Ymaze, novel object recognition, and Morris water maze tests to evaluate cognitive function. Together, our findings show that chronic phase removal of neurotoxic microglia using CSF1R inhibitors after experimental TBI can markedly reduce chronic neuroinflammation and neurodegeneration, as well as related long-term motor and cognitive deficits. Thus, CSF1R inhibition may provide a clinically feasible approach to limit posttraumatic neurodegeneration and neurological dysfunction following head injury.with neurobehavioral assessment and histology. Rodney M. Ritzel contributed with experimental design, collected and performed data analysis of flow cytometry; James P. Barrett contributed to data collection and PCR analysis; Sarah J. Doran contributed to data collection and IHC analysis; Yun Jiao performed nanostring data analysis; Jennie B. Leach contributed to nanostring data analysis; Gregory L. Szeto contributed to nanostring data analysis and manuscript preparation; Bogdan A. Stoica contributed with experimental design; Alan I. Faden contributed with manuscript preparation; David J. Loane contributed to study conception and design, and manuscript preparation. All authors read and approved the manuscript prior to submission.