It is difficult to localize the somatosensory cortex in children under 6 years using magnetoencephalography (MEG) with conventional median nerve stimulation. One main reason is that MEG data recorded from small children have poor signal-to-noise ratio due to their small heads and short hands. To find a better approach, this study investigated neuromagnetic activities following finger stimulation using spatially filtered MEG. Four healthy children have been studied with a whole cortex MEG system. Electric stimulation was applied to the thumb and the middle fingers with two Digital Rings. Two trials were recorded for each hand. Focal increases of spectral power were localized using spectrogram and synthetic aperture magnetometry (SAM). A clear response at a latency of 21 ms was identified in 3 children (3/4). Dipole modeling localized the somatosensory cortex in 2 children (2/4). SAM successfully localized the somatosensory cortex in 4 children (4/4). Interestingly, the functional region estimated for the thumb was significantly larger than that of the middle finger (p < 0.01). However, it is possible that this effect is due to a larger source amplitude rather than larger source volume. Our results demonstrated that the developed approach could map the somatosensory cortex in children ranging in age from 3 to 6. To our knowledge, this is the first report using non-invasive methods to provide quantitative data indicating that the functional area of the thumb is larger than that of the middle finger in small children.