It is difficult to easily estimate skeletal muscle (SM) volume in children. We aimed to develop regression-based prediction equations to estimate the total body and regional SM volume using calliper measurements of skinfold thickness and limb circumference and to investigate the validity of these equations. In total, 142 healthy, prepubertal, Japanese children, aged 6–12 years, were divided into two groups: the model development group (sixty boys, thirty-eight girls) and the validation group (twenty-six boys, eighteen girls). Contiguous magnetic resonance images were obtained from the first cervical vertebra to the ankle joints as reference data. SM volume was calculated from the summation of the digitised cross-sectional areas. Limb and waist circumferences were measured at mid-upper arm, mid-thigh, maximal calf and at the level of umbilicus. Each girth was corrected for subcutaneous adipose tissue thickness, as estimated by skinfold thickness measurements. Skinfold thickness was measured at the posterior upper arm, anterior thigh, medial calf and lateral to the umbilicus, using callipers. Significant correlations were observed between the site-matched SM volume, measured by MRI, and each corrected girth × standing height value in the model development group. When these SM volume prediction equations were applied to the validation group, the measured total body and regional SM volume were similar to the predicted values. These results suggest that the anthropometric prediction equations developed in this study provide reliable information about the total and regional SM volume in prepubertal Japanese children, with varying degrees of estimation accuracy for each region.