Prenatal alcohol exposure causes fetal developmental abnormalities via mitochondrial dysfunction, reactive oxygen species (ROS) formation, and oxidative stress. Therefore, we aimed to investigate the potential of hesperidin as a mitochondrial protective and antioxidative agent in newborn male rats as a model for fetal alcohol syndrome (FAS). Newborn male rats were divided randomly into five groups: a sham group (receiving 27.8 ml/ kg milk solution, orally), an ethanol group (5.25 g/kg in milk solution, orally, 2-10 days after birth), an ethanol + hesperidin group (25 mg/kg/ day orally), an ethanol + hesperidin group (50 mg/kg/day orally), and an ethanol + hesperidin group (100 mg/kg/day orally). Thirty-six days after birth, newborn male rats were sacrificed and brain mitochondria were isolated using differential centrifugation. Mitochondrial toxicity biomarkers of succinate dehydrogenase (SDH) activity, mitochondrial swelling, mitochondrial membrane potential (MMP), and ROS were measured. Offspring neonatally exposed to ethanol showed a significant reduction in SDH activity, mitochondrial swelling, MMP collapse, induction of ROS formation, and lipid peroxidation in isolated mitochondria. Oral administration of hesperidin restored SDH activity, improved MMP collapse and mitochondrial swelling, and reduced ROS formation. This study demonstrates that hesperidin exerts a potent protective effect against alcohol-induced mitochondrial toxicity in the FAS model. Moreover, these findings indicate that hesperidin might be a useful compound for prevention of alcohol-induced fetal developmental abnormalities during pregnancy.