This study examined the effects of quercetin on corneal opacity caused by corneal edema by suppressing the damage on corneal endothelial cell, which was induced by mitomycin-C (MMC). In the MMC-treated group, the number of keratocytes was noticeably fewer compared to that of other groups. Although this group showed normal amount of fiber in the corneal stroma, the thickness was shown to be very thick and the alignment of the corneal endothelial cells that worked as the barrier against aqueous humor was irregular. According to such results, it was known that corneal opacity induced by MMC is not caused by proliferation of keratocytes, but by corneal edema triggered by the infiltration of aqueous humor. In the MMC+quercetin and quercetin+MMC-treated groups, the number of keratocytes was higher and polymorphonuclear leukocytes infilteration was lower significantly compared to that of the MMC-treated group. Although the amounts of fiber and endothelioid cell arrangement were normal, there was more space observed in the corneal stroma. Nonetheless, these groups showed significantly lower stromal thickness compared to that of the MMC group. In conclusion, quercetin has the effect on the reduction of corneal opacity caused by corneal edema that work MMC-induced damage to the corneal endothelial cells.