The Megacities around the world are facing a rapid growth in their markets. An increasing number of new customers are demanding more services and products in urban areas, which are often very dense and congested. However, the traditional road-based logistics strategies to supply those customers have been inadequate to deal with largely restricted delivery operations. These challenges can come up either due to legislation that restricts the travel of trucks inside the city centers or to the increasing number of medium size vehicles in the streets. This paper shows a method to compare two options to deliver the products in the city centers, one using the traditional road-based delivery, and another with a intermodal rail-road model using the public transit system. A data analysis of the city’s Master Transportation Plan shows a low level of utilization of the public transit system, allowing to study the intermodal freight transportation in that system in urban areas. Henceforth, to cope with transit time and cost, we developed a model assessing the sensitivity and opportunities analyzing the Rio de Janeiro’s case study. There is an evidence that the model is sensible to the proposed congestion factor in the transit time and it can be an approach to improve the level of service of the deliveries inside the city centers, decreasing the needed number of medium size trucks. The results have shown that is possible to use intermodal transportation when the road-based distribution operation suffers from a certain level of congestion in the haulage and in the last-mile stage.