In a satellite time management system, the GPS-based clock synchronization technique[1] has the merits of precision time management by knowing the time difference or the error between the OBT(On Board Time) of the internal processors and GPS time every second. It can be realized employing the DPLL(Digital Phase Loop Lock) and FEP(Front End Processor) circuitry for the clock synchronization[2]. In this paper, a refined DPLL & FEP scheme is proposed to provide the precision, stability and robustness of the operation, which is to compensate the errors and noise of the GPS signal, and also to cope with the case when the GPS signal is lost due to several reasons. The simulation and HIL (Hardware In the Loop) test results using the FM(Flight Model) in the course of KOMPSAT-2(Korea Multi Purpose Satellite-2) design and development are illustrated to demonstrate the salient features of this methodology.