Quantum key distribution (QKD) using polarisation encoding can be hard to implement over deployed telecom fibres because the routing geometry and the birefringence of the fibre link can alter the polarisation states of the propagating photons. These alterations cause a basis mismatch, leading to an increased quantum bit error rate (QBER). In this work we demonstrate a technique for a dynamically compensating fibre-induced state alteration in a QKD system. This compensation scheme includes a feedback loop that minimizes the QBER using a stochastic optimization algorithm. The effectiveness of this technique is implemented and verified in a polarisation entanglement QKD system over a deployed telecom fibre.