Introduction Although apical HCM has been considered to be more benign than asymmetric HCM, there is no study directly comparing long-term mortality in apical versus asymmetric HCM. Methods This retrospective study enrolled 796 patients (243 apical HCM and 553 asymmetric HCM). Electrocardiographic and echocardiographic data were analyzed. We assessed all-cause mortality using inverse probability of treatment weighted (IPTW) method and propensity score matched (PSM) analysis. Results In patients with asymmetric HCM, QT prolongation (11.1% versus 4.5%, P=0.005), QRS widening (17.7% versus 4.9%, P<0.001), PR prolongation (14.8% versus 6.2%, P=0.002), and pathologic Q wave (3.1% versus 0.4%, P=0.02) were significantly more frequent, but left ventricular strain (8.2% versus 43.0%, P<0.001) was significantly less frequent. The incidence of J wave was similar between two groups. The median follow-up duration was 6.5 years in the overall 796 patients. Apical HCM showed a similar all-cause mortality compared to those with asymmetric HCM (IPTW: P=0.05, PSM: P=0.05, 73% versus 69%, log rank P=0.38). There was no electrocardiographic predictor for the long-term outcomes. Conclusions Apical HCM was not so benign as previously known. All cause mortality rate of apical HCM was as high as that of asymmetric HCM. Abnormal electrocardiographic findings were not related to the long-term outcomes.