This paper presents a nondestructive evaluation approach for system identification (SID) of real railway bridges using field vibration test results. First, a multi-phase SID scheme designed on the basis of eigenvalue sensitivity concept is presented. Next, the proposed multi-phase approach is evaluated from field vibration tests on a real railway bridge (Wondongcheon bridge) located in Yangsan, Korea. On the steel girder bridge, a few natural frequencies and mode shapes are experimentally measured under the ambient vibration condition. The corresponding modal parameters are numerically calculated from a three-dimensional finite element (FE) model established for the target bridge. Eigenvalue sensitivities are analyzed for potential model-updating parameters of the FE model. Then, structural subsystems are identified phase-by-phase using the proposed model-updating procedure. Based on model-updating results, a baseline model and a nondestructive evaluation of test bridge are identified.