Fat-mass and obesity-associated protein (Fto) plays important roles in energy metabolism. It also acts as a demethylase and is most abundantly found in the brain. In the present study, we examined the spatial and temporal changes of Fto immunoreactivity after five minutes of transient forebrain ischemia in the hippocampus. In the control group, Fto immunoreactivity was mainly observed in the nucleus of pyramidal cells in the CA1 and CA3 regions as well as the polymorphic layer, granule cell layer, and subgranular zone of the dentate gyrus. Fto immunoreactivity was transiently, but not significantly, increased in the hippocampal CA3 region and the dentate gyrus two days after ischemia compared to mice without ischemia in the sham-operated group. Four days after ischemia, low Fto immunoreactivity was observed in the stratum pyramidale of the CA1 region because of neuronal death, but Fto immunoreactive cells were abundantly detected in the stratum pyramidale of the CA3 region, which is relatively resistant to ischemic damage. Thereafter, Fto immunoreactivity progressively decreased in the hippocampal CA1 and CA3 regions and the dentate gyrus until ten days after ischemia. At this time-point, Fto immunoreactivity was significantly lower in the hippocampal CA1 and CA3 regions and the dentate gyrus compared to that in the sham-operated group. The reduction of Fto immunoreactive structures in the hippocampus may be associated with impairments in Fto-related hippocampal function.