A single photon detection system and method are disclosed which have a control block for helping to monitor and optimize performance, especially at high detection rates. The system is based on photon detectors constructed with avalanche photodiodes (APD) gated in time to operate in the Geiger mode. An electrical reference frequency is generated which is subtracted from the APD output in order to better isolate the breakdown event. The resulting signal is sampled and analyzed to allow the control unit to optimize the magnitude and phase of the electrical reference frequency. The control unit may also change the gate pulse shape and phase, including by the use of a digital-to-analog converter. The gate pulse can be shifted off an input optical pulse so as to estimate dark count rate, or shifted to measure a reference input signal to estimate detection efficiency.