We present a neonatal case with intractable atrial flutter that did not respond to digitalization and electrical cardioversion. Intravenous flecainide administration completely resolved the atrial flutter. Proarrhythmic effects were not induced by flecainide administration. Although the efficacy of flecainide for atrial flutter during the infantile or childhood period is low, intravenous flecainide is worth consideration as a treatment for atrial flutter, even in intractable cases as described here, during the neonatal period.