Damage of embankments during earthquakes is widely attributed to the liquefaction of foundation soil. Previous studies have investigated the dynamic response of embankments by mainly considering uniform sand foundation and a single earthquake event. However, the foundation of an embankment consists of many sublayers of soil from liquefiable sand to relatively impermeable layer, and during earthquakes a mainshock may trigger numerous aftershocks within a short time which may have the potential to cause additional damage to soil structures. Accordingly, the investigation of liquefaction-induced deformation of earthen embankments on various liquefiable foundation conditions under mainshock–aftershock sequential ground motions is carried out by a series of dynamic centrifuge tests in this study. The liquefiable foundation includes uniform sand profile, continuous layered soil profile, and non-homogeneous soil profiles. Effects of various foundation conditions on embankment deformations are compared and analyzed. From the test results, it is found that the embankment resting on non-homogeneous soil deposits suffer more damage compared to the uniform sand foundation of same relative density. The test results also suggest that the sequential ground motions have a significant effect on the accumulated deformation of embankment.