Railway embankments in floodplains are always at a high risk of damage due to floods. The risk is however doubled when the region is seismically active. Embankment failures caused by multiple hazards like earthquakes and floods are common and are not limited to infrastructure downtime. Hence, evaluating the risk posed to existing railway embankments becomes crucial. This study is a part of the broad work that investigates the failure process of railway embankments under some common flooding scenarios and strong ground motions, separately and also considers the combined effect of both. This article discusses the seismic risk assessment of an embankment through non-linear dynamic analysis and two-dimensional (2D) numerical modeling. Both the embankment and its foundation are treated as a layered profile and the response at each layer is recorded in terms of peak acceleration of that layer. The peak acceleration of each layer is used to get the overall deformation pattern of the embankment. The reliability of the structure is also assessed through fragility analysis, which is performed using incremental dynamic analysis (IDA) with peak ground acceleration (PGA) as the intensity measure and maximum vertical displacement of the crest as the damage index. A comparison of the probability of exceedance of damage indices is also drawn considering two different intensity measures, PGA of input motions and peak acceleration response of individual layers. The results highlight the importance of proper response analysis in assessing the seismic behavior of embankments.