This paper proposes a real-time embedded system for joint space control of omnidirectional mobile robots. Actuators driving an omnidirectional mobile robot are connected in a line topology which requires synchronization to move simultaneously in translation and rotation. We employ EtherCAT, a real-time Ethernet network, to control servo controllers for the mobile robot. The first part of this study focuses on the design of a low-cost embedded system utilizing an open-source EtherCAT master. Although satisfying real-time constraints is critical, a desired trajectory on the center of the mobile robot should be decomposed into the joint space to drive the servo controllers. For the center of the robot, a convolution-based path planner and a corresponding joint space control algorithm are presented considering its physical limits. To avoid obstacles that introduce geometric constraints on the curved path, a trajectory generation algorithm considering high curvature turning points is adapted for an omnidirectional mobile robot. Tracking a high curvature path increases mathematical complexity, which requires precise synchronization between the actuators of the mobile robot. An improvement of the distributed clock—the synchronization mechanism of EtherCAT for slaves—is presented and applied to the joint controllers of the mobile robot. The local time of the EtherCAT master is dynamically adjusted according to the drift of the reference slave, which minimizes the synchronization error between each joint. Experiments are conducted on our own developed four-wheeled omnidirectional mobile robot. The experiment results confirm that the proposed system is very effective in real-time control applications for precise motion control of the robot even for tracking high curvature paths.