This paper presents a real-time motion control system using EtherCAT protocol and its application on a differential drive mobile robot. The motion controller is designed from open-source components consisting of dual kernel approach using standard Linux and real-time extension of Xenomai, and the EtherCAT Master stack, IgH. In order to validate feasibility of the real-time system, timing analysis between the master and the slaves is performed in terms of periodicity of the cyclic task, jitter, and in-control execution time as test metrics. Furthermore, we conducted a convolution based trajectory planning algorithm that considers the physical limits of the mobile robot to generate periodic velocity commands following a curved path. Encoder data from each wheels is evaluated to guarantee the accuracy of the motion control system in Cartesian space.