During smoking, nicotine, the most bountiful compound in cigarettes, is absorbed into the body by the lungs and quickly metabolized in the liver, causing three major adverse impacts such as toxic, neoplastic, and immunomodulatory effects. Saponins extracted from several plants are reported to exhibit various biological actions, such as anticancer effects. So, the potential protective effect of fenugreek saponin and nanofenugreek saponin against toxicity induced by nicotine in male rats was investigated in this study. Animals were exposed to nicotine (1.5 mg/kg/day) and/or treated with fenugreek saponin (25, 50, and 100 mg/kg/day) and nanofenugreek saponin (20, 40, and 80 mg/kg/day). Comet assays, histopathological examination, and analyses for the expression levels of glutamate aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1) genes in liver tissues as well as the activity of glutathione peroxidase (GPx) and glutathione-S-transferase (GST) were conducted. The results revealed that nicotine treatment induced a significant increase in DNA damage, decrease in the expression levels of (GLAST) and (GLT-1) genes, and increase in histopathological alterations in liver tissues. Moreover, nicotine treatment induced a significant reduction in the activity of antioxidant enzymes GPx and GST. On the other hand, administration of fenugreek saponin or nanofenugreek saponin with nicotine significantly decreased the DNA damage, increased the expression levels of (GLAST) and (GLT-1) genes, and decreased histopathological alterations in liver tissues. Additionally, a significant increase in the activities of GPx and GST was observed. The results suggested that DNA damage and histological injuries induced by nicotine were decreased by the administration of fenugreek saponin or nanofenugreek saponin; thus, fenugreek saponin and nanofenugreek saponin can be used as ameliorative agents against nicotine toxicity.