Fetal magnetocardiography (fMCG) allows the non-invasive recording of fetal cardiac electrical activity with increasing efficacy as gestation progresses. Many reports on the successful extraction of reliable fetal magnetocardiographic traces in singleton pregnancies exist in the literature, whereas there is only one report on the reconstruction of averaged fetal cardiac signals obtained in a twin pregnancy with the use of a double sensor array system. In this paper, we aimed at assessing the effectiveness of an ICA-based procedure to reconstruct the time course of fetal cardiac signals recorded with a single-shot multi-channel fMCG device in an uncomplicated twin pregnancy at 27 weeks. The evaluation of heart rate and beats synchronicity permitted the differentiation of fetal components; the quality of reconstructed fetal signals allowed visual inspection on single cycles and the simultaneous monitoring of separate fetal heart rate patterns. The proposed technique might be applied in twin pregnancies not only to characterize fetal arrhythmias, but also in all cases of discordant fetal growth, either in the case of intra-uterine growth retardation affecting one fetus, or in the case of twin-twin transfusion syndrome, a life-threatening condition where both fetuses are at risk of heart failure.