The purpose of this study was to analyze the outcomes and complications between stroke subtypes after intravenous thrombolysis. A total of 471 patients with acute ischemic stroke after intravenous thrombolysis from January 2007 to April 2014 were enrolled and classified according to the Trial of Org 10172 in Acute Stroke Treatment. A multivariate logistic regression model was used to evaluate the outcomes and complications among stroke subtypes after adjusting for baseline variables. Of the 471 patients, 117 (25.1 %) had large-artery atherosclerosis (LAA), 148 (31.8 %) had cardioembolism (CE), 82 (17.6 %) had small vessel disease (SVD), 119 (25.5 %) had undetermined etiology, and 5 (1.1 %) had other determined etiology. The patients with SVD had the mildest initial stroke severity and highest ratio of good and favorable outcomes, whereas those with CE had a higher rate of symptomatic intracranial hemorrhage (sICH) than those with SVD. After adjusting for confounding factors, the ratio of favorable outcome in the patients with SVD stroke was higher than in those with LAA. SVD was associated with a significantly lower rate of any hemorrhage compared to other stroke subtypes, whereas there were no differences in sICH or mortality between stroke subtypes. A lower initial National Institutes of Health Stroke Scale score was associated with good and favorable outcomes, and lower rates of sICH and mortality. The patients with SVD after intravenous thrombolysis had better outcomes and a lower rate of hemorrhage even after adjusting for confounding factors. Stroke severity was an independent factor associated with better functional outcomes, sICH and mortality.