Purpose: To evaluate and compare the effects of subconjunctival injection of coenzyme Q10 (CoQ10) and vitamin E (Vit E) ophthalmic solution (Coqun®) with subconjunctival bevacizumab in a suture-induced corneal neovascularization (CoNV) rabbit model. Materials and Methods: CoNV was induced in the right eyes of 24 New Zealand rabbits using a 7.0 silk suture. One week after suturing, the rabbits were randomly divided into four groups and treated with a subconjunctival injection of either 0.1 mL balanced salt solution (control), bevacizumab (2.5 mg/0.1 mL), or two different doses of Coqun [(2 mg CoQ10 + 10 mg Vit E/0.2 mL) and (4 mg CoQ10 + 20 mg Vit E/0.4 mL)]. Photographs were taken on day 7 (pre-injection) and day 14 (7 days post-injection). On day 14, the regression area of CoNV was measured for analysis, and enucleation was performed for histopathological evaluation. Results: The CoNV areas after treatment were smaller in all three treatment groups compared with the control group (p < 0.01). The mean percentage of CoNV regression was highest in the bevacizumab group (87.8% ± 3.2%), followed by the Coqun groups (69.5% ± 5.9% in the 0.2 mL dose, and 67.1% ± 9.3% in the 0.4 mL dose) No significant difference was observed between the two different doses of Coqun (p = 0.99). Conclusions: Subconjunctival administration of Coqun ophthalmic solution may offer a beneficial adjunct for the treatment of CoNV. Although it is not less effective than bevacizumab, its neuroprotective properties suggest potential value in cases where CoNV and glaucoma coexist. Further clinical studies are warranted to confirm these findings and to better define its therapeutic role.