Systems and methods for operating a quantum network system. The methods comprise, by a network node: generating optical clock pulses and photons using the optical clock pulses; generating a combined signal by combining the optical clock pulses with at least some of the photons such that a consistent temporal offset exits between the optical clock pulses and the first photons and/or a wave function of each photon at least partially overlaps an envelope of a respective one of the optical clock pulses; and transmitting the combined signal over a first quantum channel in which the optical clock pulses co-propagate with the photons.