Similar predisposing factors are found in most types of atrial arrhythmias. The incidence of atrial fibrillation (AF) among patients with atrial flutter is high, suggesting similar outcomes in patients with those arrhythmias. We sought to investigate the long-term outcomes and prognostic factors of patients with AF and/or atrial flutter with contemporary management using radiofrequency ablation. In an academic institution, we retrospectively examined the clinical course of 8,962 consecutive patients admitted to our department with a diagnosis of AF and/or atrial flutter. After a median follow-up of 934 ± 1,134 days, 1,155 deaths and 715 stroke and/thromboembolic (TE) events were recorded. Patients with atrial flutter undergoing cavotricuspid isthmus ablation (n = 875, 37% with a history of AF) had a better survival rate than other patients (hazard ratio [HR] 0.35, 95% confidence interval [CI] 0.25 to 0.49, p <0.0001). Using Cox proportional hazards model and propensity score model, after adjustment for main other confounders, ablation for atrial flutter was significantly associated with a lower risk of all-cause mortality (HR 0.55, 95% CI 0.36 to 0.84, p = 0.006) and stroke and/or TE events (HR 0.53, 95% CI 0.30 to 0.92, p = 0.02). After ablation, there was no significant difference in the risk of TE between patients with a history of AF and those with atrial flutter alone (HR 0.83, 95% CI 0.41 to 1.67, p = 0.59). In conclusion, in patients with atrial tachyarrhythmias, those with atrial flutter with contemporary management who undergo cavotricuspid isthmus radiofrequency ablation independently have a lower risk of stroke and/or TE events and death of any cause, whether a history of AF is present or not.