Time synchronization between distributed embedded systems in the Real Time Locating System (RTLS) based on Time Difference of Arrival (TDOA) is one of the most important factors to consider in system design. Clock jitter error between each system causes many difficulties in maintaining such a time synchronization. In this paper, we implemented a system to synchronize clocks between FPGA based distributed embedded systems using the recovery clock of CDR (clock data recovery) used in high speed serial communication to solve the clock jitter error problem. It is experimentally confirmed that the cumulative time error that occurs when the synchronization is not performed through the synchronization logic using the CDR recovery clock can be completely eliminated.