Objective: To assess the cerebral vasomotor response to ipsilesional repetitive transcranial magnetic stimulation (rTMS) on transcranial Doppler (TCD) in patients with recent ischemic stroke without carotid occlusive disease, and to compare this response in patients with cortical and subcortical infarcts. Methods: Consecutive patients with first-ever anterior circulation acute ischemic stroke (<3 days) and no extra- or intracranial arterial stenosis were prospectively recruited. Patients were divided into 2 groups: cortical infarct (CI, n = 15) and subcortical infarct (SI, n = 16). TCD cerebral blood flow velocity (CBFV) and pulsatility index were measured before and after 10-Hz suprathreshold rTMS over the dorsolateral prefrontal cortex. Results: ANOVA showed a greater percentage increase in middle cerebral artery (MCA) CBFV in the SI group than in the CI group following rTMS (p = 0.01). The percentage change in CBFV was significantly correlated between both MCAs in SI patients but not in CI patients (r = 0.8, p < 0.001 vs. r = 0.05, p = 0.9, respectively). Conclusions: 10-Hz rTMS induces significant bilateral hemodynamic changes in patients with acute ischemic stroke, which appear to be less prominent and less synchronous in patients with cortical infarcts. These findings may allow optimization of the use of TMS in acute stroke.