A case of fetal atrial flutter successfully recorded by magnetocardiography (MCG) is reported. Initial ultrasonography revealed frequent fetal atrial extrasystoles at 31 weeks of gestation. Fetal MCG was recorded using a multichannel MCG system at 31, 35 and 38 weeks of gestation. A series of fluctuations in the baseline of the MCG were noted at 35 and 38 weeks of gestation, which were revealed to be atrial flutter P waves. The averaged MCG showed that the fetal arrhythmia was an atrial flutter with a 3:1 atrioventricular block. The diagnosis was confirmed by neonatal electrocardiogram. Fetal MCG may be useful for the diagnosis of fetal atrial flutter.