Fetal cardiac time intervals (fCTI) are dependent on fetal growth and development, and may reveal useful information for fetuses affected by growth retardation, structural cardiac defects or long QT syndrome. Fetal cardiac signals with a signal-to-noise ratio (SNR) of at least 15 dB were retrieved from fetal magnetocardiography (fMCG) datasets with a system based on independent component analysis (ICA). An automatic method was used to detect the onset and offset of the cardiac waves on single cardiac cycles of each signal, and the fCTI were quantified for each heartbeat; long rhythm strips were used to calculate average fCTI and their variability for single fetal cardiac signals. The aim of this work was to compare the outcomes of this system with the estimates of fCTI obtained with a classical method based on the visual inspection of averaged beats. No fCTI variability can be measured from averaged beats. A total of 25 fMCG datasets (fetal age from 22 to 37 weeks) were evaluated, and 1768 cardiac cycles were used to compute fCTI. The real differences between the values obtained with a single cycle analysis and visual inspection of averaged beats were very small for all fCTI. They were comparable with signal resolution (+/-1 ms) for QRS complex and QT interval, and always <5 ms for the PR interval, ST segment and T wave. The coefficients of determination between the fCTI estimated with the two methods ranged between 0.743 and 0.917. Conversely, inter-observer differences were larger, and the related coefficients of determination ranged between 0.463 and 0.807, assessing the high performance of the automated single cycle analysis, which is also rapid and unaffected by observer-dependent bias.