Background Previous research indicates disparities in atrial fibrillation (AF) recurrence and complications following catheter ablation in women; however, long-term outcomes based on gender remain underexplored. Objective This study evaluated the long-term rates of AF recurrence and major adverse cardiovascular and cerebrovascular events (MACCE) following catheter ablation, investigating gender-related risk factors to inform clinical practice improvement. Methods We conducted a retrospective analysis using data from a prospectively observational registry of AF ablation procedures at our institution from 2015 to 2020. Patients were followed up for MACCE and AF recurrence. The risk factors of AF recurrence and MACCE were further explored. Results The study cohort consisted of 2,293 patients, including 1,441 males and 852 females, and had an average follow-up duration of 50.36 months. After catheter ablation, females exhibited a notably higher rate of recurrence compared to males, with a hazard ratio of 1.305 and a 95% confidence interval ranging from 1.101 to 1.547, which was statistically significant (p=0.0014). Gender differences in AF recurrence persisted regardless of early versus late intervention (both p<0.05). No significant difference in MACCE rates was observed between genders. Independent risk factors for AF recurrence included female gender, diabetes, left atrial diameter ≥40 mm. Conclusions Gender differences significantly impact the long-term outcomes of AF recurrence, but not MACCE rates post-catheter ablation. The study highlights the necessity to integrate gender considerations into AF management strategies.