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Introduction: Reactive oxygen species (ROS)-mediated inflammation plays a crucial role in ischemic brain injury. Therefore, the activation of the nuclear erythroid 2 related protein and heme-oxygenase-1 (Nrf2/HO-1) pathway by thymoquinone (TQ) could ameliorate ischemic brain damage. Areas covered: The photo-thrombotic method was employed to assess the impact of TQ in attenuating ischemic brain damage in C57BL/6 J mice and thy1-YFP-16 transgenic mice. In vitro study of TQ efficiency to attenuate the oxygen-glucose deprivation/reoxygenation (OGD/R) induced cell death by fluorescence-activated cell sorting (FACs) analysis was also analyzed. The protein expression levels of Nrf2/HO-1, inflammatory, and apoptotic were evaluated by immunofluorescence and western blot techniques. Besides, mRNA expression level of inducible nitric oxide synthase (iNOS), proto-oncogene (c-MYC), proto-oncogene (c-FOS), 5-hydroxytryptamine receptors (5-HT), and autophagy-related 5 (Atg5) were evaluated by RT-qPCR. The dendritic spine density of YFP slices was determined by confocal microscope. Results: Our in vivo and in vitro results indicated that TQ significantly mitigates brain damage and motor dysfunction after ischemic stroke. These observations coincided with curtailed cell death, inflammation, oxidative stress, apoptosis, and autophagy. Most importantly, Nrf2/HO-1 signaling pathway activation by TQ was vital in the modulation of the above processes. Lastly, we found TQ to have minimal toxicity in liver tissue. Conclusion: Our study gives credence to TQ as a promising intervention therapy for cerebral ischemia that decreases inflammation, oxidative stress, and neuronal cell death via the Nrf2/HO-1 pathway, along with modulation of apoptotic and autophagic processes.