Systems and methods for synchronizing the clocks of a central device and one or more destination devices are disclosed. In some embodiments the central device and destination devices are implemented in a space-based or high-altitude asset. The central device provides a series of synchronization pulses to the one or more destination devices. In response to detecting, at the destination device, the synchronization pulse, a sample of the destination device clock is stored in a register. The sample is provided to the central device. The sequence is repeated at least once. A phase offset between the central device clock and the destination device clock may be determined based on the returned samples and the position of the samples within the register.