Abstract—The paper presents a system time synchronization mechanism of a Real-Time Operating System (RTOS) for loosely coupled distributed Cyber-Physical Systems (CPS) such as distributed control systems connected with wireless networks or wide-area networks. In CPS, computations directly interact with the physical world based on the physical time. Meanwhile, application tasks that perform computation are managed by a RTOS according to the system time. Thus, a precisely synchronized system time is required for high performance control of the physical world. The system time synchronization mechanism presented in this paper provides the system time that is precisely synchronized with UTC (coordinated universal time). The system time synchronization mechanism compensates tick rate, tick phase and the value of the system time utilizing the Pulse Per Second (PPS) signal of a GNSS (global navigation satellite systems) receiver module. We build the system time synchronization mechanism into a RTOS, with which embedded computers synchronously execute application tasks according to the precisely synchronized system time. The evaluation results show that the synchronization error is sufficiently small for practical embedded control systems. The system time synchronization mechanism can be easily applied to other RTOS.