Abstract The majority of the cavotricuspid isthmus (CTI) region consists of discretely arranged muscle bundles separated by connective tissue. Heterogeneity in the anatomic arrangement of the muscle bundles results in differences in the endocardial and epicardial activation patterns. We present a case of recurrent atrial flutter (AFL) despite the presence of a complete endocardial CTI block. We found epicardial‐endocardial breakthrough (EEB) sites on the right atrial high septum. In addition, the epicardial excitation confirmed by endocardial activation mapping was detected as far‐field potentials. Radiofrequency ablation was performed at the EEB site. No AFL has recurred for 12 months after the present procedure.