Mode pairing is a crucial step for the stability of any model-updating strategy based on experimental modal parameters. Automatically establishing a stable and assertive correspondence between numerical and experimental modes, in many cases, proves to be a very challenging task, especially in situations where complex mode shapes are present. This article presents a novel formulation for the automatic mode pairing between experimental and numerical complex modes based on an Energy-based Modal Assurance Criterion (EMAC). The efficiency of the proposed criterion was demonstrated on the basis of a case study involving the pairing between numerical and experimental modes of a passenger railway vehicle. A highly complex detailed FE numerical model of the vehicle was developed involving the modeling of the carbody, bogies and axles. A numerical damped modal analysis allowed obtaining the main global rigid-body and flexural modes of the vehicle’s carbody, as well as several local modes associated to the vibration of specific components of the carbody. Due to the localized damping provided by the suspensions, these modes presented complex modal ordinates, especially for the rigid-body modes. The comparison between the results obtained from the application of the EMAC and the classical MAC criteria, on the pairing of five global mode shapes, proved that the EMAC criterion is much more assertive, avoiding mismatches between the experimental global modes and some of the local numerical modes with similar configurations, and, consequently, establishing the correct correspondences between experimental and numerical modes.