Limited data exist regarding the outcome of atrial fibrillation (AF) surgery and catheter ablation in patients with hypertrophic cardiomyopathy (HCM). The purpose of this study was to evaluate the safety and efficacy of nonpharmacologic treatment of AF in HCM. One hundred forty-seven patients (46 female, age 55 ± 11 years, ejection fraction EF 58% ± 8%) with symptomatic paroxysmal (58%), persistent (31%), and long-standing persistent AF (11%) refractory to antiarrhythmic drugs who presented for their first catheter ablation (n = 79) or AF surgery (n = 68) were included. After follow-up of 35 months (interquartile range 13, 60), 29% of patients who underwent catheter ablation and 51% of those who had undergone AF surgery had no documented recurrent atrial arrhythmia after a single procedure. Repeat ablation was performed in 55% of patients with recurrent arrhythmia in the catheter group and 24% in the surgery group, increasing the success rate to 39% and 53%, respectively, after 1 or more procedures. Predictors of success after the first procedure in a multivariable setting included higher baseline EF and male gender. Persistent or long-standing AF and log of AF duration were associated with lower success. Major complications occurred in 6% of the catheter ablation group and 18% of the AF surgery group. During follow-up, 16 patients died (9 in catheter group, 7 in surgery group) and 1 underwent heart replacement. Lower baseline EF and older age were independently associated with death. Catheter ablation and AF surgery are associated with symptomatic improvement in HCM patients. However, long-term success is lower and complications are higher than previously reported.