A method of autocalibrating the timing of the laser in a quantum key distribution (QKD) system is disclosed. The laser generates photon signals in response to a laser gating signals from a controller. The method includes first performing a laser gate scan to establish the optimum laser gating signal arrival time corresponding to an optimum bit-error rate when exchanging photon signals between encoding stations of the QKD system. Once the optimum laser gating signal arrival time is determined, the laser gate scan is terminated and laser gate dithering is initiated. Laser gate dithering involves varying the arrival time of the laser gating signal around the optimum value of the arrival time. Laser gate dithering provides minor adjustments to the laser gating signal arrival time to ensure that the system operates at or near the optimum bit-error rate.