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<i>Aspergillus flavus</i> is the most common etiology of fungal endophthalmitis in India, while <i>Candida albicans</i> is the causative agent in the West. In this study, we determined the role of microglial cells in evoking an inflammatory response following an infection with <i>A. flavus</i> and <i>C. albicans</i> strains isolated from patients with endophthalmitis. Microglia (CHME-3) cells were infected with <i>A. flavus</i> and <i>C. albicans</i> and the expression of Toll-Like Receptors (TLRs), cytokines and Matrix metalloproteinases (MMPs) were assessed at various time intervals. <i>A. flavus</i> infected cells induced higher expressions of TLR-1, -2, -5, -6, -7 and -9 and cytokines such as IL-1α, IL-6, IL-8, IL-10 and IL-17. In contrast, <i>C. albicans</i> infected microglia induced only TLR-2 along with the downregulation of IL-10 and IL-17. The expression of MMP-9 (Matrix metalloproteinase-9) was however upregulated in both <i>A. flavus</i> and <i>C. albicans</i> infected microglia. These results indicate that microglial cells have the ability to incite an innate response towards endophthalmitis causing fungal pathogens via TLRs and inflammatory mediators. Moreover, our study highlights the differential responses of microglia towards yeast vs. filamentous fungi.