Systems and methods for compensating a QKD system for variations in temperature are disclosed. One of the methods includes identifying an optimum detector gating signal timing as a function of temperature for a single-photon detector (SPD) control board in one of the QKD stations. The detector gating signal timing versus temperature information is stored in a look-up table in a memory unit. The QKD system's temperature is monitored during operation and the timing of the detector gating signal is adjusted based on the operating temperature and the corresponding timing value adjustment in the look-up table. The result is a compensated detector gating timing signal provided to the SPD that yields an optimum number of photon counts even as the temperature of the QKD station varies.