The present study investigated the synergistic effects of radiofrequency ablation and various anticoagulants on adverse outcomes in patients with atrial fibrillation (AF) and left atrial appendage thrombosis following successful thrombolysis. Patients diagnosed with AF and left atrial appendage thrombosis post-successful thrombolysis (n=92) were retrospectively analysed. They were divided into two groups: Group A received radiofrequency ablation combined with an anticoagulant, while Group B received an anticoagulant alone and in combination with antiarrhythmic drugs. Subgroup analyses were conducted based on left atrial diameter (>45 mm), duration of AF (>1 year) and types of anticoagulants. Univariate and multivariate logistic regression analyses were performed to assess stroke and mortality risks in patients with AF with left atrial appendage thrombosis after dissolution. Multivariate logistic regression analysis identified AF duration (>1 year), left atrial diameter (>45 mm) and BNP level as significant risk factors for stroke (P<0.05). Compared with NOACs, the traditional anticoagulants (warfarin) demonstrated higher survival rates and lower stroke incidence in Group B (P<0.05); however, no significant difference was observed within Group A (P>0.05). Radiofrequency ablation combined with anticoagulants appeared to be more effective in treating AF with left atrial appendage thrombosis post-dissolution compared with anticoagulants alone. Attention to AF duration and left atrial diameter is crucial during early patient management. However, the choice between warfarin or NOACs for patients with AF and left atrial appendage thrombosis warrants further investigation.