Background and Aim of the Study The midterm clinical outcomes of patients with latent left ventricular outflow tract (LVOT) obstruction who undergo septal myectomy are unclear. Therefore, this study aimed to evaluate the clinical outcomes of patients with latent LVOT obstruction who underwent septal myectomy. Methods We studied 34 patients with hypertrophic cardiomyopathy (HCM) and latent LVOT obstruction who underwent septal myectomy in 2011–2019 at Anzhen Hospital. After 2:1 propensity score matching, the study cohort included 34 patients with latent LVOT obstruction and 68 patients with resting LVOT obstruction. Results Compared to patients with resting LVOT obstruction, patients with latent LVOT obstruction had a thinner interventricular septal thickness (18.2 ± 3.2 mm vs. 20.4 ± 5.6 mm; p = .01), while the proportion of moderate or severe mitral regurgitation was significantly higher (26.5% vs. 5.9%; p = .003). Moreover, the proportion of mitral valve procedures (26.5% vs. 5.9%; p = .004) was significantly higher in patients with latent LVOT obstruction. However, there was no intergroup difference in cardiovascular death (5.9% vs. 1.5%, p = .26). Furthermore, the 5‐year survival rates after sudden cardiac death (100.0% vs. 91.7%; p = .26) and cardiovascular death (95.5% vs. 89.0%; p = .32) were similar between HCM patients with latent versus resting LVOT obstruction. Conclusions Midterm clinical outcomes were similar and excellent in a matched cohort of HCM patients with latent versus resting LVOT obstruction after septal myectomy.