The thesis’s main objective is to develop mathematical models and algorithms for optimising two important supply chain management problems, namely the warehouse order picker routing problem and the multi-commodity network design problem. The second chapter of this thesis presents a graph reduction algorithm for solving the Travelling Salesman Problem in a planar grid graph applied in the order picking problem. The proposed algorithm applies to any other problem with a planar grid graph. In the third chapter, a more general and realistic case of order picking within modern warehouses is considered with scattered storage policies. In this chapter, a mathematical formulation is presented for the Generalized Travelling Salesman Problem and in larger instances, a Guided Local Search algorithm is proposed. The third chapter is focused on a variant of multi-modal Multi-commodity Network design problems with delivery time, hub capacities, stochastic demand and express delivery.