Purpose Renal ischemia-reperfusion injury (RIRI) may occur secondary to several reasons leading to renal failure. Coenzyme-Q10 (CoQ10) is a well-known antioxidant. However, the effects CoQ10 against RIRI have not been evaluated. Our aim was to evaluate protective effects of CoQ10 to renal ischemia-reperfusion by biochemical, immunohistochemical and scintigraphic findings. Methods Thirty Wistar-albino rats were randomly separated into groups of 10; Group Sham; Group ischemia-reperfusion (IR) had left renal pedicle clamping; Group CoQ10+IR had IR and CoQ10. Twenty-four hours later after reperfusion, scintigraphy was performed and after that, rats were sacrificed. To demonstrate effects of RIRI, serum urea and creatinine levels and tissue levels oxidative stress markers were evaluated. Both kidneys were subjected to histopathological evaluation and to confirm RIRI-induced immunohistochemical aspects of apoptosis, terminal-deoxynucleotidyl-transferase mediated-deoxyuridine-triphosphate-nick-end-labeling assay and caspase-3 were assessed. Results Tissue oxidative stress, histopathologic changes, apoptosis scores and quantitative scintigraphic parameters were significantly higher in Group IR compared with Group Sham. Although tissue oxidative stress levels and histopathologic changes were not significant, quantitative scintigraphic parameters of contralateral kidney of Group IR were significantly increased. Compared with Group IR, Group CoQ10+IR presented decreased tissue oxidative stress levels; decreased scores of histopathology and apoptosis; and decreased quantitative scintigraphic parameters with increased split renal function in ischemic kidney. Conclusions Our results suggest that other than its antioxidant properties, CoQ10 shows antiperoxidative, antiapoptotic and antiinflammatory potential in protecting renal functioning of ischemic kidney. Furthermore, our results show that renal scintigraphy is a feasible method to detect early changes in renal functioning after RIRI.