Background Atrial fibrillation (AF) is an important risk factor for thromboembolic events, for which catheter ablation represents an effective therapy for rhythm control. Intuitively, ablation may reduce the incidence of thromboembolism, but data is quite limited. Hypothesis Catheter ablation was associated with the fewer risk of thromboembolism compared with nonablation in patients with AF. Methods A systematic search was performed in PubMed, EMBASE, the Web of Science, and the Cochrane Library from inception to September 2019. Random-effects model was used to estimate the risk ratios (RR) for the thromboembolic events between the ablation and nonablation groups. Results Twenty-five studies (12 randomized controlled trials and 13 observational studies) with 104 687 participants were included. Pooled analysis suggested that ablation was associated with a 35% lower risk of total thromboembolic events compared to nonablation group (RR = 0.65; 95% CI, 0.51-0.82;P= .0003). When separated into early-phase (<30 days) and late-phase (>30 days) events, ablation was associated with an increased early-phase thromboembolism (RR = 1.96; 95% CI, 1.35-2.83;P= .0004) but a decreased late-phase thromboembolism (RR = 0.75; 95% CI, 0.63-0.90;P= .002). Subgroup analysis according to different study types found similar results were found in observation studies, but not in RCT studies because the sample size was too small to be conclusive. Conclusions In patients with AF, catheter ablation was associated with a fewer risk of overall and late-phase thromboembolism in comparison with nonablation. However, over the early postoperative period, catheter ablation was associated with the double higher risk of thromboembolic events.