The aim of the present study was to evaluate the change in corneal protein and oxidative stress state after using photodynamic therapy (PDT) for treatment of experimental corneal neovascularization (NV) with benzoporphyrin derivative (BPD). One group was considered as control (N = 10 eyes), corneal NV was induced in 25 New Zealand male rabbits (N = 50 eyes) after placing silk sutures in the corneal limbus. Five rabbits with corneal NV were left without any treatment, and 20 rabbits were administered by intravenous injection with Verteporfin at a dose of 1.5 mg/kg. Diode laser (660 nm) was applied for 5 minutes with a power of 50 mW/cm2. For a period of 4 weeks, five rabbits were selected and sacrificed weekly (N = 10 eyes each). The corneas were isolated for determination of protein content, SDS-PAGE, total antioxidant capacity (TAC), total oxidative capacity (TOC), malondialdhyde (MDA) and oxidative stress index (OSI). The results indicated that corneal NV induced changes in the content and composition on the corneal protein and gradual improvement of the cornea after the 3rd and 4th week of PDT was detected. Furthermore, the oxidative/antioxidative balance shifted towards the antioxidative status that helped to prevent further damage.