BMI itself is a lousy proxy for physical fitness - just ask weightlifters - and it has to be calibrated to the physical scale of adult human beings, so I can't see how it could properly apply to small children. It's better to use the standard height/weight charts to see where a given child falls compared to other children (i.e. in terms of percentile).
EDIT: For example, the charts found here, and in particular the boys and girls aged 2-20 charts.