Atrial fibrillation (AF) in hypertrophic cardiomyopathy (HCM) patients is highly associated with deterioration of their clinical condition, such as worsening heart failure symptoms, and an increased thromboembolic stroke risk and cardiac mortality rate. This study aimed to investigate the long-term clinical course after catheter ablation (CA) in HCM patients with AF. Among 566 primary HCM patients at our institution, 94 who underwent rhythm control therapy to manage AF from 2002 to 2016 were retrospectively analyzed. The eligible patients were divided into two groups: those who managed AF with CA (n = 34) and those without CA (n = 60). The endpoints were the incidence of initial clinical events, including HCM-related death or an unplanned heart failure hospitalization, or new-onset thromboembolic strokes. During a mean follow-up of 5.8 years, 6% in the CA group and 28% in the non-CA group had a progression of the AF type into permanent AF (Log-rank: p = 0.012). In the Kaplan-Meyer curve analyses, the incidence of clinical events was significantly lower in the CA group than non-CA group (p = 0.025). The annual rates for the incidence of clinical events were 1.2% in the CA group and 6.7% in the non-CA group. In a Cox multivariate analysis, CA therapy (adjusted hazard ratio 0.22; 95% confidence interval: 0.05–0.97; p = 0.046) was the only independent predictor of the incidence of clinical events. In conclusion, CA may be associated with a favorable long-term clinical course in HCM patients with AF.