Obstructive sleep apnea syndrome (OSAS) is an independent risk factor for ischemic cerebrovascular diseases, and results in worse prognosis and higher mortality. We aimed to investigate the effects of early treatment of OSAS on the prognosis of ischemic stroke. We prospectively evaluated patients with acute supratentorial ischemic stroke and OSAS on admission (acute stage), at second week (subacute stage) and at second month (chronic stage); 11 (73.3%) out of 15 patients put on the non-invasive mechanical ventilation treatment within 48 h of stroke constituted the treatment group, and 13 patients constituted the control group. Patients with OSAS treatment showed significantly better prognosis and better functioning in activities of daily living in both subacute and chronic stages. The rate of shrinkage of the ischemic lesion was higher in the treatment group, though not significant. The early and effective treatment of OSAS provides a better clinical prognosis in ischemic stroke. The beneficial effects on radiological parameters need to be further studied.