We present a case of supraventricular tachycardia affecting one fetus in a twin pregnancy. Before and after treatment with flecainide and cardioversion, we examined conduction times and heart rate variability (HRV) in both twins on the basis of magnetocardiography. Cardiac conduction times increased in both fetuses but HRV showed opposing effects with a number of HRV measures. This case demonstrates that magnetocardiography not only enables identification of fetal arrhythmia, but also permits the investigation of the effects of antiarrhythmic treatment on the conductive system as well as on interaction with the autonomic nervous system.