Impaired left atrial appendage ejection fraction (LAA-EF) and peak LAA flow velocity (LAA-FV) are associated with high thromboembolic risks in patients with atrial fibrillation (AF). Herein, we examined LAA function among patients with atrial flutter (AFL) stratified by the CHA2DS2-VASc score using transesophageal echocardiography (TEE). Of 231 consecutive patients with typical AFL, 84 who fulfilled the inclusion criteria were enrolled. Among them, 57 had ongoing AFL and were divided into the isolated AFL (n = 38) and AFL with paroxysmal AF (PAF) (n = 19) groups, depending on whether they had sporadic AF before TEE. The remaining 27 patients with spontaneous sinus rhythm during TEE were designated as controls. Both the LAA-FV (31.9 cm/s vs. 51.5 cm/s, P = 0.004) and LAA-EF (28.4% vs. 36.5%, P = 0.024) measured during AFL were significantly lower in the AFL + PAF group than in the isolated AFL group. Significant inverse correlations between the CHA2DS2-VASc score and LAA-EF were identified in the AFL (P = 0.008) and AFL + PAF (P = 0.032) groups. We observed progressive LAA dysfunction in patients with AFL + PAF compared with that in patients with isolated AFL, and the LAA-EF was inversely correlated with the CHA2DS2-VASc score in these patients. Our findings may have implications on the application of thromboprophylactic therapy in patients with AFL.