5-Aza-deoxycytidine (5-aza-dC) confers neuroprotection in ischemic mice by inhibiting DNA methylation. Zebularine is another DNA methylation inhibitor, less toxic and more stable in aqueous solutions and, therefore more biologically suitable. We investigated Zebularine's effects on brain ischemia in a rat middle cerebral artery occlusion (MCAo) model in order to elucidate its therapeutic potential. Male Wistar wild-type (WT) rats were randomly allocated to three treatment groups, vehicle, Zebularine 100 μg, and Zebularine 500 μg. Saline (10 μL) or Zebularine (10 μL) was administered intracerebroventricularly 20 min before 45-min occlusion of the middle cerebral artery. Reperfusion was allowed after 45-min occlusion, and the rats were sacrificed at 24-h reperfusion. The brains were removed, sliced, and stained with 2% 2,3,5-triphenyltetrazolium chloride (TTC) before measuring infarct size. Zebularine (500 μg) reduced infarct volumes significantly (p < 0.05) by 61% from 20.7 ± 4.2% in the vehicle treated to 8.1 ± 1.6% in the Zebularine treated. Zebularine (100 μg) also reduced infarct volumes dramatically by 55 to 9.4 ± 1.2%. The mechanisms behind this neuroprotection is not yet known, but the results agree with previous studies and support the notion that Zebularine-induced inhibition of DNA methyltransferase ameliorates ischemic brain injury in rats.