A method and system for transmitting optical clock signals and quantum key signals on a single optical channel, and for reducing quantum bit error rate in a quantum key distribution system. The method includes receiving a multi-photon optical clock signal at an electro-optic switch at a first clock rate. The electro-optic switch may be configured for an interval defined by a second clock rate for generating a single photon quantum key signal. The multi-photon optical clock signal and the single photon quantum key signal may be combined such that the single optical channel transmits the single photon quantum key signal at a first interval and the multi-photon optical clock signal at a second interval. The quantum key signal may be transmitted from a transmitter at a first timing, and detected by a detector at a receiver. An output signal of the detector may be sampled at a second timing that is delayed relative to the first timing for reducing quantum bit error rate.