Intestinal Ischemia-Reperfusion (I/R) is a complex phenomenon causing local and remote tissue destruction and multiple-organ dysfunction. The present study investigates the effect of thymoquinone and omega-3 on intestinal I/R-induced hepatic dysfunction. Sixty four Wistar albino rats were randomly allocated into four experimental groups: sham control, intestinal I/R control, thymoquinone (10 mg/kg) and omega-3 (300 mg/kg) pretreated groups respectively. Intestinal I/R model were established by clamping the superior mesenteric artery for 30 min followed by 60 min reperfusion. Serum levels of aspartate Amino Transferase (AST), Alanine Aminotransferase (ALT) and Alkaline Phosphatase (ALP) were measured. Hepatic tissue contents of Malondialdehyde (MDA), reduced Glutathione (GSH), Myeloperoxidase (MPO) and Tumor Necrosis Factor alpha (TNF-α) and Superoxide Dismutase (SOD) activity were measured. Apoptosis in hepatic tissue cells was determined by immunities to chemical analysis of caspase-3. Hepatic histopathological examination was carried out. Intestinal I/R elevated serum AST, ALT and ALP levels. In-addition, hepatic tissue SOD activity and GSH content were decreased, while MDA, MPO and TNF-α contents were increased. Pre-treatment with thymoquinone or omega-3 corrected the histopathological changes and serum AST, ALT, ALP levels as well as hepatic tissue activity of SOD and GSH contents. In-addition, hepatic tissue contents of MDA and MPO were decreased. Furthermore, immunohistochemical examination showed remarkable activation of caspase-3 activity in hepatic tissue after intestinal I/R, which were corrected by thymoquinone or omega-3 pre-treatment. The protective potential of thymoquinone and omega-3 on hepatic dysfunction could be attributed to the known antioxidant, antiapoptotic and anti-inflammatory effects of test drugs.