The present disclosure is directed to a system and method for measuring small frequency differences between two signals quickly and with high precision. In particular examples, an offset between two clock signals on a satellite can be accurately determined in a time period enabling rapid clock synchronization useful in position, navigation, and tracking (PNT) and satellite communications applications. The system and method may also be implemented in constellation of cooperative satellites or other space-borne and high-altitude assets, wherein a plurality of such assets are accurately time-synchronized and more accurate ensemble average calculations are enabled using two-way time transfer (TWTT) protocols. A particular application presently disclosed measurement and correction of very small frequency differences between an atomic clock signal and a tunable clock signal.