Neuroinflammatory processes mediated by microglial activation and subsequent neuronal damage are the hallmarks of traumatic brain injury (TBI). As an inhibitor of the macrophage-inducible C-type lectin (Mincle)/spleen tyrosine kinase (Syk) signaling pathway, BAY61-3606 (BAY) has previously demonstrated anti-inflammatory effects on some pathological processes, such as acute kidney injury, by suppressing the inflammatory macrophage response. In the present study, the potential effects of BAY on microglial phenotype and neuroinflammation after TBI were investigated. BAY (3 mg/kg) was first administered into mice by intraperitoneal injection after TBI induction in vivo and microglia were also treated with BAY (2 mu M) in vitro. The levels of inflammatory factors in microglia were assessed using reverse transcription-quantitative PCR and ELISA. Cortical neuron, myelin sheath, astrocyte and cerebrovascular endothelial cell markers were detected using immunofluorescence. The levels of components of the Mincle/Syk/NF-kappa B signaling pathway [Mincle, phosphorylated (p)-Syk and NF-kappa B], in addition to proteins associated with inflammation (ASC, caspase-1, TNF-alpha, IL-1 beta and IL-6), apoptosis (Bax and Bim) and tight junctions (Claudin-5), were measured via western blotting and ELISA. Migration and chemotaxis of microglial cells were evaluated using Transwell and agarose spot assays. Neurological functions of the mice were determined in vivo using the modified neurological severity scoring system and a Morris water maze. The results of the present study revealed that the expression levels of proteins in the Mincle/Syk/NF-kappa B signaling pathway (including Mincle, p-Syk and p-NF-kappa B), inflammatory cytokines (TNF-alpha, IL-1 beta and IL-6), proteins involved in inflammation (ASC and caspase-1), apoptotic markers (Bax and Bim) and the tight junction protein Claudin-5 were significantly altered post-TBI. BAY treatment reversed these effects in both the cerebral cortex extract-induced cell model and the controlled cortical impact mouse model. BAY was also revealed to suppress activation of the microglial proinflammatory phenotype and microglial migration. In addition, BAY effectively attenuated TBI-induced neurovascular unit damage and neurological function deficits. Taken together, these findings provided evidence that BAY may inhibit the Mincle/Syk/NF-kappa B signaling pathway in microglia; this in turn could attenuate microglia-mediated neuroinflammation and improve neurological deficits following TBI.