The stability of railway embankments under extreme storms is important for ensuring the normal operation of the railway network. In this study, the effect of precipitation extremes on the stability of the high-speed railway embankment in China is investigated. Historical records of precipitation in the region along the Xuzhou–Shanghai section are used to estimate the value of probable maximum precipitation. Three extreme storm scenarios are generated by upscaling the base storm event which occurred in July 2016 in Nanjing. The results of the numerical analysis show that the water levels rise up significantly, and the lower part of the embankment near the toe is fully saturated. The slip surface moves to shallow depths, and the factor of safety reduces due to surface infiltration. The effects of track superstructures, filling materials in the substructure and the uncertainties of soil hydraulic properties are also discussed. Under extreme storms, a ballastless embankment can be marginally stable even though the embankment surface is covered with a concrete base. The extreme storm magnifies the effects of the uncertainty of soil properties, and the uncertainty bounds of factor of safety are wider under a more severe storm.