Low recanalization rates and poor clinical outcome have been reported after intravenous thrombolysis (IV-tPA) in carotid-T occlusion (CTO). We studied clinical outcome and imaging findings of MRI-based intravenous thrombolysis in CTO. Data of patients with acute ischemic stroke and CTO treated with IV-tPA within 6 h of symptom onset based on MRI criteria were retrospectively analyzed. Vessel occlusion was defined based on MR angiography. Acute diffusion and perfusion lesion volumes and final infarct volumes after 3-7 days were delineated. The National Institutes of Health Stroke Scale (NIHSS) was used to assess the neurological deficit on admission. Recanalization was evaluated after 24 h. Clinical outcome was assessed using the modified Rankin Scale (mRS) after 90 days. Clinical and imaging data were compared to patients with middle cerebral artery main stem occlusion (MCAO). A total of 20 patients with CTO and 51 patients with MCAO were studied. Onset to treatment time, NIHSS on admission, initial diffusion and perfusion lesion volumes, and recanalization rates after 24 h were similar between groups. Final infarct volume was larger for CTO (82 vs. 30 ml, p = 0.006). Although overall outcome was not significantly different between groups (p = 0.251), independent outcome (mRS 0-2) tended to be less frequent in CTO (17 vs. 39 %), while poor outcome (mRS 4-6) appeared more common (72 vs. 43 %). The proportion of patients with good clinical outcome after intravenous thrombolysis in CTO is small. Moreover, final infarct volume is larger and clinical outcome appears to be worse compared to MCAO.