A system and method of synchronizing clocks in a distributed network is disclosed. A simple 1-pulse-per-second timing pulse is routed to time-stamping units in each network device and utilized to measure traffic-dependent synchronization packet residence delays within network elements. Synchronization messages are updated to reflect the measured residence times, thus creating transparent clocks that can readily be synchronized across the network. The simple timing pulse architecture allows the method to be applied readily both to new designs and to retrofit existing hardware.