Introduction: Atrial fibrillation (AF) is a common arrhythmia in patients with hypertrophic cardiomyopathy (HCM) and is associated with renal function deterioration. The protective effects of catheter ablation (CA) of AF on the renal function in HCM patients remains unsolved. Methods: From 2009 to 2020, 169 consecutive patients with HCM and AF (age 70±12, 87 males) were retrospectively evaluated. The estimated glomerular filtration rate (eGFR) was evaluated at the study enrollment or one month before the CA and reevaluated three months and 12 months later. Results: Among the 169 patients, 63 underwent CA of AF (ablation group) and the remaining 106 did not (control group). After propensity score matching, 45 pairs were matched. The baseline eGFR was similar between the two groups (P=0.83). During a mean follow-up period of 34±27 months, sinus rhythm was maintained in 36 (80%) patients after 1.7±0.8 ablation procedures. The eGFR significantly decreased from baseline to three months (P<0.01) and from baseline to one year (P<0.01) in the control group, while the eGFR in the ablation group was maintained both from baseline to three months (P=0.94) and from baseline to one year (P=1.00) after the CA. The change in the eGFR between baseline and 12 months was significantly smaller in the ablation group than control group (P<0.01). After a logistic regression analysis, CA of AF was the independent predictor of an improvement of eGFR (OR: 2.81; 95% CI: 1.08-7.36 P=0.04). Conclusions: CA of AF had a protective effect on the renal function in patients with HCM.