Introduction: To assess the long-term outcome of catheter ablation in patients with hypertrophic cardiomyopathy (HCM), especially in patients with apical CM(ApHCM). Methods and results: From 9,249 AF ablation cases, 97 patients (28 with ApHCM and 69 with non-ApHCM) were enrolled. Another 97 patients matched by age, AF type, AF duration, and left atrial diameter were selected as the control group. After a mean follow-up of (44.3 +/- 29.6) months, success rate after a single procedure was 42.9% in the ApHCM patients (P = 0.725), 36.2% in the non-ApHCM patients (P = 0.136) versus 50.5% in the control group. After multiple procedures, success rate both in the ApHCM group (50%, P = 0.047) and in the non-ApHCM group (50.4%, P = 0.017) were lower than in the controls (68.0%). More patients in the ApHCM and in the non-ApHCM group suffered very late recurrence beyond 1 year after the index procedure. Left atrial diameter (hazard ratio [HR] 1.04, 95% confidential interval [CI] 1.01-1.08, P = 0.018) and AF duration (HR 1.01,95% CI 1.00-1.01, P = 0.005) were independent predictors of recurrence after the index ablation. There was no difference in thromboembolic events between the HCM group and the control group (8.2% vs. 3.1%, P = 0.082). Conclusions: Patients with ApHCM or non-ApHCM had similar success rate of AF ablation after single procedure and lower success rate after multiple procedure compared with the control group.