Quantifying characteristics of movement is needed for providing effective coaching to develop talent in sports. This study aimed to clarify differences in motor commands in more- and less-skilled boy sprinters and to investigate equilibrium regulation via changes in muscle activity and kinematics during performance. In this pilot study involving five 10–11-year-old boy children who regularly participate in lessons at the Mizuno running school, we collected electromyography and kinematics data during 30-meter and 50-meter field track sprints. A U.S.-patented synergy analyzer was then applied to estimate the equilibrium point (EP)-based co-activation synergies and the concomitant virtual trajectory in the configuration space. Results showed the counterintuitive control of lower limbs by children when they are sprinting; inter-limb asymmetry of equilibrium regulation achieves similar kinematic limb movement. In the virtual trajectory in one leg, the equilibria after foot-strike were regulated intermittently during the early- and mid-swing phases. In the virtual trajectory in the other leg, the equilibria after foot-strike were regulated continuously during these swing phases. The less-skilled child runners showed a delayed equilibrium action response in both types of virtual trajectories during the early- and mid-swing phases. Information on gait asymmetry would be beneficial not only for coaching to improve sprint training but also from clinical and injury perspectives. These findings provide insights for “tailor-made” coaching based on the type of leg control during sprinting.