A lack of co-contraction may predispose to knee instability or laxity, resulting in additional shear stress on the internal structures of the knee, especially in below-knee amputee (BKA) subjects. The purposes of this study were: (1) to provide information on how BKA children regulate agonist and antagonist muscle coordination, and (2) to quantify the level of knee co-contraction in able-bodied (AB) and BKA children during the stepping-in-place (SIP) task. Fourteen children (7 BKA vs. 7 AB), paired for age, weight and height, participated in this study. One-way ANOVA with Newman–Keuls post hoc tests ( p < 0.05) were used to compare peak power, the co-contraction index, and the resultant agonist and antagonist moments during different phases of SIP. Statistical analysis revealed that BKA children perform the task with similar kinematics than AB children while they generated less co-contraction in both their non-amputated limb and amputated limb, notably because the two groups of children used different agonist and antagonist muscles during the same periods of the SIP. This lack of co-contraction may reduce knee stability and may stress the internal structures of the knee in both the NAL and AL, and may lead to the development of premature knee osteoarthritis.