Background/Objectives: The risks of blood clot formation, stroke, heart failure (HF), and cardiovascular death are enhanced in individuals with atrial flutter (AFL). However, it remains unclear whether left atrial appendage thrombus (LAAT) in individuals with AFL with anticoagulation enhances the risk of cardiovascular morbidity and mortality. Thus, in the current trial, we aimed to evaluate the predictive role of LAAT for cardiovascular outcomes in individuals with AFL who were receiving anticoagulation and admitted for electrical cardioversion. Methods: Ninety patients were included in this prospective observational cohort study. The primary endpoint was the identification of LAAT by transesophageal echocardiographic examination. All participants were observed for a median of 2114.5 (interquartile range, 1487.5–2591) days to identify the secondary endpoints: cardiovascular death, transient ischemic attack (TIA), stroke, systemic thromboembolic complications, hospitalization due to HF, or myocardial infarction. Results: LAAT was identified in nine (10%) patients. No differences in cardiovascular outcomes between patients with and without LAAT were documented. However, a higher CHA2DS2-VASc score, previous myocardial infarction, and previous stroke/TIA/systemic thromboembolism were associated with significantly higher rates of hospitalization due to HF. Decreased left ventricular ejection fraction (LVEF) was associated with significantly higher rates of cardiovascular death, underscoring the significance of this marker in disease prognosis. Conclusions: The impact of LAAT on cardiovascular outcomes was insignificant. Higher CHA2DS2-VASc scores, previous myocardial infarction, previous stroke/TIA/systemic thromboembolism, and lower LVEF significantly affected long-term prognosis and were associated with a poor prognosis.