This study examined the hemodynamic effects of craniectomy compared to reperfusion on the temporal evolution of cerebral perfusion in different brain regions in a rat model of focal cerebral ischemia. Three groups were investigated: no treatment, reperfusion or craniectomy at 1 h. Perfusion-weighted magnetic resonance imaging (PWI) was performed serially from 0.5 to 6 h. Relative regional cerebral blood flow was calculated for different regions and infarct volume was assessed by histology at 24 h. As conclusion, both, craniectomy and reperfusion increased cerebral perfusion in the acute phase of cerebral ischemia. While reperfusion resulted in a homogeneous improvement of perfusion in the cortex and basal ganglia, craniectomy improved only cortical perfusion in areas directly under the craniectomy site. PWI is well suited to non-invasively monitor perfusion alterations after aggressive therapeutical approaches in stroke.