In this paper we demonstrate an active polarization drift compensation scheme for optical fibres employed in a quantum key distribution experiment with polarization encoded qubits. The quantum signals are wavelength multiplexed in one fibre along with two classical optical side channels that provide the control information for the polarization compensation scheme. This set-up allows us to continuously track any polarization change without the need to interrupt the key exchange. The results obtained show that fast polarization rotations of the order of 40π rad s–1 are effectively compensated for. We demonstrate that our set-up allows continuous quantum key distribution even in a fibre stressed by random polarization fluctuations. Our results pave the way for Bell-state measurements using only linear optics with parties separated by long-distance optical fibres.