Objective: We conducted this study to explore the possible protective effect of 2-aminoethoxydiphenyl borate (2-APB) on experimentally induced optic nerve injury in an acute ischemia-reperfusion (AIR) model. Materials and Methods: A total of 30 Wistar albino rats were randomly divided into sham, AIR, and AIR+treatment (AIR10) groups. In the sham group, AIR model was not created. In the AIR group, AIR model was created without the administration of drug. In the AIR10 group, 2-APB was administered 10 min before reperfusion. Results: Tissue samples were subjected to histological, immunohistochemical, and electron microscopic procedures. Histopathological examination revealed intense hypertrophic cells, more glial cells, capillary dilatation, and intense demyelination areas in the AIR group compared to those in the sham and AIR10 groups. Immunohistochemical staining demonstrated an increase in Orai1 and STIM1 immunoreactivity in the AIR group but less intense staining in the AIR10 group. Electron microscopy revealed injury in optic nerve axons in the AIR group, whereas this type of injury occurred to a lesser extent in the AIR10 group. Conclusion: In rats, store-operated Ca2+ entry in the cell had an essential role in optic nerve ischemia-reperfusion injury, and 2-ABP may have a protective effect on optic nerve injury caused due to AIR. Cite this article as: Demirci T, Bilge N, Ucar M, Ozgul Abuc O, Atilay H. Electron Microscopic and Immunohistochemical Examination of the Effect of 2-Aminoethoxydiphenyl Borate on Optic Nerve Injury in A Rat Model. Eurasian J Med 2020; 52(1): 61-6.