In this work we develop an analysis of polarization control schemes suitable for quantum key distribution systems.
Both time division multiplexing and wavelength division multiplexing based schemes are considered. A model
for the optimization of the temporal separation between reference pulses and polarization encoded photons
is presented. The model accounts for the reference pulse shape, the single photon detector gate width, and
the respective temporal separation between them. The theoretical results are validated through experimental
measurements. These results can be used to optimize the performance of polarization control schemes and
therefore to optimize the polarization encoded quantum key distribution systems.