Atrial fibrillation (AF) frequently complicates hypertrophic cardiomyopathy (HCM) and is associated with significant morbidity and mortality. Catheter ablation (CA) has emerged as an effective treatment modality; however, its efficacy compared to medical therapy in HCM patients remains unclear. We conducted a systematic review and meta-analysis to assess the impact of CA compared with medical therapy on hard prognostic outcomes in patients with HCM and AF. PubMed, Scopus, and Cochrane databases were systematically searched for randomized controlled trials and observational studies comparing CA with medical therapy alone in HCM patients with documented AF. We Included studies that reported at least 1 clinical outcome of interest over a minimum 5-year follow-up period: all-cause mortality, cardiovascular death, heart failure hospitalizations and stroke. A random-effects model was applied, and heterogeneity was assessed by I² statistics. We analyzed 4 studies comprising a total of 570 patients, 316 (55%) of whom underwent CA. CA significantly reduced heart failure hospitalizations compared to medical therapy alone (RR 0.37; 95% CI 0.16 to 0.87; p = 0.02). However, CA showed no statistically significant effect on all-cause mortality (RR 0.68; 95% CI 0.41 to 1.11; p = 0.12), cardiovascular death (RR 0.66; 95% CI 0.35 to 1.25; p = 0.20), or stroke incidence (RR 0.29; 95% CI 0.03 to 2.61; p = 0.27). In conclusion, in patients with HCM and AF, CA is associated with a significant reduction in heart failure hospitalizations compared to medical therapy alone, without a significant impact on all-cause mortality, cardiovascular death, or stroke.