The evaluation of the short-term effect of topically applied coenzyme Q10 (CoQ10) on retina and choroid in Alzheimer's disease (AD) was aimed in this study. Randomized controlled study included a total of 93 patients, 62 of whom with AD. Thirty (32.3%) AD patients received treatment (Group 1), 32 (34.4%) AD patients observed without treatment (Group 2), and Group 3 included 31 (33.3%) healthy controls (HC). Neurological and ophthalmological examinations including optical coherence tomography (OCT) were executed. Retinal nerve fiber layer (RNFL) thickness in all quadrants increased following CoQ10 treatment in Group 1; however significant rise yielded in average and temporal quadrant RNFL thickness. Average and superonasal sector ganglion cell-inner plexiform layer (GCIPL) thickness increased significantly following CoQ10 treatment. The correlation analysis between difference in pre- and posttreatment OCT values in Group 1 revealed that rise in average RNFL thickness was inversely correlated with duration of the disease and rise in average GCIPL thickness and superonasal sector thickness was inversely correlated with severity of the disease. Short-term topical CoQ10 resulted in improvement in AD related retinal ganglion cell (RGC) loss which may reflect the salvage of some RGCs in the reversible transitional phase. More bioavailability through intravitreal route of administration and longer duration of effect with sustained release forms may possibly help enhalting the RGC loss, especially incipience of neurodegenerative diseases.