The major cause of earthquake damage to an embankment is the liquefaction of the soil foundation that induces ground level deformations. The aim of this paper is to assess numerically the effect of the liquefaction-induced settlement of the soil foundation on an levee due to real earthquakes. The seismic vulnerability is evaluated in terms of analytical fragility curves constructed on the basis of non-linear dynamic Finite Elements (FE) analysis. However, FE analysis can be expensive due to very large number of simulations needed for an accurate assessment of the system failure behaviour. This problem is addressed by building a Gaussian Process (GP) emulator to represent the output of the expensive FE model. A comparison with the FE reference results suggests that the proposed GP model works well and can be successfully used as a predictive tool to compute the induced damage on the levee. Findings also illustrate clearly the importance and the advantages of an adequate definition of the input parameters to built the GP model.