We investigated whether thymoquinone (TQ) exerts a beneficial effect on renal injury due to amikacin (AK) administration in rats. To generate kidney damage with AK, a single 1.2 g/kg dose of AK was administered intraperitoneally. TQ was administered orally to the AK treated group at a dose of 40 mg/kg for five days. At the end of the experiment, rats were sacrificed and blood samples were used to measure blood urea nitrogen (BUN) and creatinine (Cr) levels. Kidney samples were taken to measure the oxidative stress biomarker, malondialdehyde (MDA), and expression of the antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT). Because reactive oxygen species (ROS) and apoptosis contribute to tissue damage associated with NADPH oxidase (NOX), we also investigated NOX-2, NOX-4 and apoptosis marker, caspase-3, expression using immunohistochemistry. MDA, BUN, Cr, NOX-2, NOX-4 and caspase-3 production were increased, and SOD and CAT were decreased in the AK treated group compared to controls. MDA, BUN, Cr, NOX-2, NOX-4 and caspase-3 levels were decreased, and SOD and CAT levels were increased in TQ + AK treated rats compared to AK treated animals. TQ appears to protect the kidney from the toxic effects of AK.