A method of synchronizing the operation of a two-way QKD system by sending a sync signal (SC) in only one direction, namely from one QKD station (ALICE) to the other QKD station (BOB). The one-way transmission greatly reduces the amount of light scattering as compared to two-way sync signal transmission. The method includes phase-locking the sync signal at BOB and dithering the timing of the quantum signals so as to operate the QKD system in three different operating states. The number of detected quantum signals is counted for each state for a given number of detector gating signals. The QKD system is then operated in the state associated with the greatest number of detected quantum signals. This method is rapidly repeated during the operation of the QKD system to compensate for timing errors to maintain the system at or near its optimum operating state. The method allows for only having to adjust the timing of a single timed element--namely, the quantum laser--to compensate for timing variations, rather than having to adjust the timing of all or some of the timed elements in the QKD system.