The science of cities aims to model urban phenomena as aggregate properties that are functions of a system’s variables. Following this line of research, this study seeks to combine two well-known approaches in network and transportation science: (i) The macroscopic fundamental diagram (MFD), which examines the characteristics of urban traffic flow at the network level, including the relationship between flow, density, and speed. (ii) Percolation theory, which investigates the topological and dynamical aspects of complex networks, including traffic networks. Combining these two approaches, we find that the maximum number of congested clusters and the maximum MFD flow occur at the same moment, precluding network percolation (i.e. traffic collapse). These insights describe the transition of the average network flow from the uncongested phase to the congested phase in parallel with the percolation transition from sporadic congested links to a large, congested cluster of links. These results can help to better understand network resilience and the mechanisms behind the propagation of traffic congestion and the resulting traffic collapse.