Multiple sclerosis (MS) leaves millions of people worldwide with impaired central nervous system (CNS) function. To make matters worse, a great deal is still unknown about the physiological landscape of MS pathogenesis and of what factors might exacerbate or ameliorate the severity of disease outcomes. As the resident immune cell of the CNS, microglia are considered active members of this pathogenic landscape, but whether their contributions are more destructive or protective remains controversial. Using the microglia-depleting drug PLX5622, an inhibitor of colony stimulating factor 1 receptor (CSF1R), it was demonstrated that upon depletion of microglia in mice infected with the neurotropic JHM strain of the mouse hepatitis virus (JHMV) results in an increase in viral load and severity of demyelination with a hindered capacity to remyelinate. Additionally, single-cell RNA sequencing (scRNAseq) revealed that microglia depletion prior to JHMV infection results in increased expression of transcripts associated with disease, including Apoe, Trem2, and Spp1 (osteopontin), and reduced expression of remyelination associated transcripts Igf1 (insulin-like growth factor-1), Lpl (lipoprotein lipase), and Cst7 (cystatin F) in macrophage populations and remaining microglia. However, the mechanisms by which microglia reduce the severity of demyelination and overall disease outcome is not yet understood. ScRNAseq was employed to apprehend the heterogeneous populations of cells at defined times post-infection in the pathogenic landscape following CNS infection with JHMV. Results exposed a subpopulation of microglia that have elevated expression of remyelination markers Igf1, Lpl, and Cst7, that are present at day 21 p.i., in chronic disease, when remyelination efforts are occurring. Cystatin F expression drastically increases in microglia when demyelination occurs and has been associated with remyelination in various pre-clinical models of demyelination and is even found overlapping with remyelinating areas of MS plaques in human post-mortem tissue. As microglia phagocytosis of compact myelin results in increased expression of Cst7, cystatin F may act as a signaling mediator to negatively regulate the inflammatory environment that causes demyelination. Therefore, we chose to investigate whether the effects of microglia on reducing demyelination and promoting remyelination were mediated through microglia expression and secretion of cystatin F. Using a cystatin F germline KO mouse (Cst7 KO), we demonstrated that JHMV infection of the CNS results in more severe clinical disease in mice lacking Cst7 when compared with infected wild-type littermates (WT), which correlated with a significant increase in demyelination in Cst7 KO mice at both day 14 and 21 p.i as well as impaired remyelination at day 21 p.i. Genetic ablation of cystatin F did not impact acute disease with no impairment in control of virus replication or effect on immune cell infiltration into the CNS at day 7 p.i. relative to WT littermates. However, at day 21 p.i., we found increased infiltration of CD8+, CD4+, and virus specific CD4+ T cells into spinal cords. Consistently, scRNAseq on CD45+ cells from spinal cords of uninfected and infected Cst7 KO and WT littermates revealed increased expression of T cell chemoattractant Cxcl9 by microglia and macrophages and increased expression of activation markers for CD4+ T cells (Icos, Ifng, Tnfrsf4) and CD8+ T cells (Gzmb, Prf1, Ifng). Furthermore, expression of disease-associated transcripts Apoe and Trem2 were elevated in microglia and monocyte/macrophage populations. Together, these findings indicate that cystatin F plays a role in chronic JHMV-induced disease by restricting the severity of demyelination and promoting remyelination, potentially through negative regulation of T cell recruitment an activation. Results from this research provide further insight into the roles of microglia in disease and repair in a pre-clinical model of chronic MS and illuminate a potential mechanism for microglia in contributing to repair.