Females with atrial fibrillation (AF) are at increased risk for ischemic stroke but have been under-represented in AF ablation cohorts. Whether the incidence of TE in women after catheter ablation is higher is unknown. We aimed to analyze the predictive value of thromboembolic scores and other clinical variants for thromboembolism (TE) after AF catheter ablation, separately in women and men. TE was combined endpoint of early (within first month) and late (during long-term follow-up) stroke, transient ischemic attack, or systemic embolism. Oral anticoagulation was prescribed for 6 months after catheter ablation and discontinued if CHADS(2) was < 2 and no AF recurrences were documented. The study population (n = 2,069, 66 % male, 60 +/- A 10 years; 62 % paroxysmal AF) was followed for a median of 18 months (IQR 12-29). Overall 31 TE (1.5 %) occurred with 16 events within 30 days of ablation and 15 TE during the follow-up. Fourteen females (2.0 %) and 17 males (1.2 %) suffered TE (p = 0.128). On multivariate analysis, higher CHADS(2) (HR 1.65, 95 % CI 1.10-2.47, p = 0.015), CHA(2)DS(2)-VASc (HR 1.42, 95 % CI 1.03-1.96, p = 0.034), R(2)CHADS(2) (HR 1.76, 95 % CI 1.32-2.35, p < 0.001) scores, and eGFR < 60 ml/min/1.73 m(2) (HR 3.95, 95 % CI 1.23-12.7, p = 0.021) were significantly associated with TE in men. In females, LV-EF (HR 0.95, 95 % CI 0.91-0.99, p = 0.021) and CHA(2)DS(2)-VASc score (HR 1.52, 95 % CI 1.01-2.28, p = 0.044) remained significant predictors for TE. TE rates after AF catheter ablation are low in both genders. In females, LV-EF and CHA(2)DS(2)-VASc score and in males all three scores and renal dysfunction were associated with TE.