Background: N-terminal pro-brain natriuretic peptide (NT-proBNP) levels are a promising biomarker for predicting stroke outcomes; however, their prognostic validity is not well-understood in patients who have undergone intravenous thrombolysis. This study was designed to evaluate the prognostic value of NT-proBNP levels in patients with acute ischemic stroke treated with intravenous thrombolysis.Methods: Patients with ischemic stroke who underwent intravenous thrombolysis between April 2015 and December 2020 were analyzed. Demographic information, information related to intravenous thrombolysis, medical history, and laboratory test results were collected. Outcomes, such as hemorrhagic transformation, early neurologic deterioration, poor 3-month functional outcomes, and 3-month mortality were recorded. Correlations between NT-proBNP levels and the above outcomes were analyzed, an individualized prediction model based on NT-proBNP levels for functional outcomes was developed, and a nomogram was drafted.Results: A total of 404 patients were included in the study. Elevated NT-proBNP levels were independently associated with hemorrhagic transformation, poor 3-month functional outcomes, and 3-month mortality, while early neurological deterioration was not. An association between NT-proBNP levels and hemorrhagic transformation was noted. An individualized prediction model for poor functional outcomes was established, which was composed of ln(NT-proBNP), National Institutes of Health Stroke Scale (NIHSS), and baseline glucose, with good discrimination [area under the curve (AUC) 0.764] and calibration (P > 0.05).Conclusion: To the best of our knowledge, this is the first report on the association between NT-proBNP levels and hemorrhagic transformation in patients who have undergone intravenous thrombolysis. The 3-month functional outcomes and mortality were found to be associated with NT-proBNP levels. An individualized prediction model based on NT-proBNP levels to predict the 3-month functional outcomes was established. Our results suggest that NT-proBNP levels could be used as a prognostic biomarker in patients with acute ischemic stroke treated with intravenous thrombolysis.