Autophagy activation exerts neuroprotective effects in the ischemic stroke model. Ezetimibe (Eze), a Niemann–Pick disease type C1-Like 1 (NPC1L1) pharmacological inhibitor, has been reported to protect hepatocytes from apoptosis via autophagy activation. In this study, we explored whether Eze could attenuate neuronal apoptosis in the rat model of middle cerebral artery occlusion (MCAO), specifically via activation of the AMPK/ULK1/autophagy pathway. Two hundred and one male Sprague-Dawley rats were subjected to transient MCAO followed by reperfusion. Eze was administered 1 h after MCAO. To elucidate the underlying molecular mechanism, Dorsomorphin, a selective AMPK inhibitor, and 3-methyladenine (3-MA), an autophagy inhibitor, were injected intracerebroventricularly before MCAO. Infarct volume, neurological score, brain cholesterol levels, immunofluorescence staining, Western blot, and Fluoro-Jade C (FJC) staining were used to evaluate the effects of Eze. The endogenous NPC1L1 expression increased and mainly expressed in neurons after MCAO. Intranasal administration of Eze reduced brain infarct volume at 24 and 72 h after MCAO, with improved short and long-term neurological functions after MCAO. Eze reduced brain cholesterol levels (total cholesterol, free cholesterol and cholesteryl esters) and the number of FJC-positive neurons. The expression of phosphorylated AMPK (p-AMPK) and downstream ULK1, Beclin1, LC3BII, Bcl-2, and Bcl-xl increased, while P62 and proapoptotic Bax decreased after treatment with Eze. Pretreatment with Dorsomorphin and 3-MA reversed the beneficial effects of Eze. These findings suggest that intranasal administration of Eze plays neuroprotective role through autophagy activation after MCAO in rats. Lowered cholesterol levels and AMPK activation may act in conjunction to induce autophagy after treatment with Eze. Eze merits further investigation as a potential therapeutic agent in ischemic stroke patients.