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NT-proBNP level is a predictive factor in hypertrophic cardiomyopathy patients, in which left ventricular outflow tract obstruction contributes to an increased NT-proBNP level. However, studies regarding the influence of septal myectomy on NT-proBNP level in hypertrophic obstructive cardiomyopathy are lacking.One hundred and eighty-two patients who underwent septal myectomy in Fuwai Hospital from May 2011 to March 2016 and were included in the present study. Preoperative and follow-up NT-proBNP was retrospectively collected. Correlation analysis was performed to determine the factors affecting preoperative NT-proBNP and postoperative decrease.The cohort had a median age of 46.2 [IQR: 36.5-53.1] years, and 106 (58.2%) patients were male. NT-proBNP decreased to 816.5 [IQR: 400.3-1661.8] pg/mL from preoperative 1732.4 [IQR: 819-3296.5] pg/mL (p<0.001). Baseline NT-proBNP was correlated with gender (p<0.001), maximum septal thickness (p<0.001), and resting pressure gradient (p=0.006). The extent of NT-proBNP decrease was positively correlated with age (p<0.001), baseline NT-proBNP (p<0.001), follow-up time (p=0.020), and enlargement of the ascending aorta (p=0.019). NT-proBNP exhibited a persistent decrease after myectomy.Myectomy significantly reduced NT-proBNP level in hypertrophic obstructive cardiomyopathy patients, in which a time-dependent manner of decrease indicated myocardial remodeling of the heart after myectomy.