In a city-scale network, trips are made in thousands of origin-destination (OD) pairs connected by multiple routes, resulting in a large number of alternatives with diverse characteristics that influence the route choice behaviour of the travellers. As a consequence, to accurately predict user choices at full network scale, a route choice model should be scalable to suit all possible configurations that may be encountered. In this article, a new methodology to obtain such a model is proposed. The main idea is to use clustering analysis to obtain a small set of representative OD pairs and routes that can be investigated in detail through computer route choice experiments to collect observations on travellers behaviour. The results are then scaled-up to all other OD pairs in the network. It was found that 9 OD pair configurations are sufficient to represent the network of Lyon, France, composed of 96,096 OD pairs and 559,423 routes. The observations, collected over these nine representative OD pair configurations, were used to estimate three mixed logit models. The predictive accuracy of the three models was tested against the predictive accuracy of the same models (with the same specification), but estimated over randomly selected OD pair configurations. The obtained results show that the models estimated with the representative OD pairs are superior in predictive accuracy, thus suggesting the scaling-up to the entire network of the choices of the participants over the representative OD pair configurations, and validating the methodology in this study.