For many years, brain ischemia has been known to be a leading cause of adult neurological disorder. In particular, many reports have shown that hyperexcitability of neurons and inflammatory response of the glia induced by ischemic reperfusion (I/R) determine the fate of cells in the ischemic core and the penumbra region. Although there are many reports on the activation and roles of signal transducer and activator of transcription (STAT) proteins (STAT1, STAT3, and STAT5) during hyperexcitation in the neuron and inflammation occurring following I/R, the temporal and spatial activation of STAT6 protein in the ischemic cortex still remain elusive. In this study, using a transient rat middle cerebral artery occlusion model, we primarily investigated the time-course expression of the phosphorylated STAT6 (pSTAT6) in the ischemic core region following I/R, which was compared with that of pSTAT3. We found that pSTAT6 significantly decreases at 1 and 12 h following I/R, whereas pSTAT3 markedly increases at each follow-up time point. In addition, the level of pSTAT6 is reduced in the ischemic core in comparison with the penumbra region at 12 h following I/R. However, there is no significant difference in pSTAT3 expression between the ischemic core and the penumbra. Taken together, our data suggest that pSTAT6 and pSTAT3 are modulated differently following I/R during ischemic stroke.