In this paper, an integrated approach is proposed that incorporates the road network design problem and the vehicle routing problem, which are very often studied separately. This approach can be adopted when the routes to follow in a transport system have to be designed (e.g., for public transit with fixed and variable routes, or for freight distribution) jointly with the network topology and capacity. The goal is to minimise congestion and the impacts on the network from passengers and freight vehicles. The design (control) variables consist of the optimal vehicle routes and optimised road network; they are both discrete (link topology for passenger and freight, routes for passengers and freight vehicles, etc.) and continuous (link capacity in terms of reserved lanes, signal settings, etc.). The problem is modelled in congested transportation networks (e.g., in an urban centre). A heuristic algorithm is adopted to find the best network configuration and the best vehicle routes. The proposed model and the adopted algorithm are applied in a test system to analyse the limits of the methodology, to verify the advantage obtained from the joint method and its applicability. In the test system, the joint procedure gives good results in terms of cost decreases. The reported methods can help public and private stakeholders in making decisions regarding transportation policy, especially in the urban environment.