Multiple Sclerosis (MS) is a devastating, incurable neurodegenerative disease affecting 3 million individuals globally. There remains an especially strong need for elucidating mechanisms of chronic inflammation in MS. I explored whether MS4A6A and its murine orthologue Ms4a6c, genes known to regulate CNS macrophages, could modulate the neuroimmune response in MS. I found that MS4A6A was strongly upregulated in macrophages from MS patient lesions. I then investigated the effect of Ms4a6c-knock-out (6C-KO) on the EAE model of MS. I found that 6C-KO mice had partial mitigation of paralysis and brain T-cell infiltration, but a nearly complete reversion of microglial inflammation and activation. This MS4A-dependent microglial phenotype was recapitulated in humanized MS4A6A-knock-in versus 6A-KO EAE mice. I performed adoptive transfer of cells from EAE donors into naïve recipients and found a large effect of donor genotype on clinical severity, suggesting Ms4a6c may modulate the ability of peripheral monocytes to induce antigen-reactive T-cells. There was also a donor-independent effect of genotype on microglial activation, indicating a distinct CNS-specific role of Ms4a6c in microglia. To investigate this, I employed the Cuprizone model of oligodendrocyte toxicity and found that 6C-KO mice had reduced microglial activation and demyelination. I also found that 6C-KO microglia phagocytosed significantly less myelin in vitro. Lastly, I showed that Ms4a6c and MS4A6A both regulate ligand-mediated microglial calcium influx, identifying a putative mechanism by which these genes modulate activation. Together, these findings indicate MS4A6A as a key regulator of peripheral and CNS-resident macrophage activation, and as a promising therapeutic target in MS.