Effective treatment of corneal epithelial defects is crucial to prevent secondary infectious keratitis and visual impairment due to loss of corneal transparency. Therefore, it is important to determine the effect of different topical agents on corneal wound healing response. The aim was to compare the effects of three different eye drops on corneal epithelial wound healing in an experimental model. Twenty-four eyes of 24 female BALB/c mice were included. A 2 mm central corneal epithelial defect was created. Topical Coenzyme Q10 + Vitamin E D-α-TPGS 4 × 1 was applied to Group A (n = 6), topical Sodium hyaluronate + Xanthan Gum + 0.3% Nethylmicine 4 × 1 to Group B (n = 6) and topical Sodium hyaluronate 4 × 1 to Group C (n = 6). Group D (n = 6) was the control group without treatment. Clinical scoring according to corneal fluorescein staining and histopathological evaluations was performed. Clinical scores according to corneal fluorescein staining were similar in all groups on days 1 (p = 0.05), 2 (p = 0.15) and 3 (p = 0.62). Electron microscopy revealed disruption of intercellular junctions between corneal epithelial cells and intracellular vacuole formation in all groups except Group A. Corneal epithelial thickness and superficial epithelial microvillus arrangement were close to normal in Group A. Although there was no difference in clinical scores between groups, electron microscopy revealed a better organised epithelium with normal configuration of microvilli and less vacuolisation in Group A.