There is concern about possible radiation damage to the eyes from occupational exposure and medical procedures. In this study, molecular mechanisms of proton radiation-induced oxidative damage to retinal cells were evaluated, with and without a cell-permeable superoxide dismutase (SOD) mimetic, metalloporphyrin compound (MnTE-2-PyP). Retinal mitochondria-associated genes and protein expression profiles were studied. Rats were treated with MnTE-2-PyP at 2.5 μg/injection into one eye 1 h before irradiation. Proton irradiation was delivered to the same eye at doses of 1 or 4 Gy and assays were done at 6 h. Levels of Bax, Bcl-2 and Sod2 proteins were evaluated by Western blot and caspase-3 immunohistochemistry was performed to confirm the occurrence of apoptosis. Expression of several genes playing central roles in regulating the mitochondrial apoptotic pathway were significantly increased after radiation exposure, including Bbc3, Bax, Bak1, Bid, and Bcl2. Among genes involved in radiation-induced oxidative stress, Sod2, Gpx and Ucp3 were up-regulated, whereas Ucp2 was down-regulated. In addition, irradiation caused changes in various proteins involved in apoptosis (caspase-3, Bax and Bcl2). Reduction in pro-apoptotic and increase in anti-apoptotic protein levels were documented after treatment with MnTE-2-PyP. Decreased activity of cytochrome c, which is involved in initiation of mitochondrial apoptosis, was also revealed after irradiation and MnTE-2-PyP. Data demonstrated that proton radiation induced mitochondrial apoptosis and altered mitochondrial function in retina. MnTE-2-PyP protected, or at least ameliorated, radiation-induced oxidative damage. These insights prompt further study of this compound as a potential therapeutic candidate for retinal protection against degenerative ocular damage induced by ionizing radiation.