This study investigates the pile damage effects on the seismic response of a base-isolated structure during soil liquefaction. Dynamic centrifuge tests are performed for a liquefiable soil and base-isolated structures with damaged and undamaged piles. The deformation of the base-isolated device is larger for the case of damaged piles than undamaged piles, which is well reproduced by the effective stress analyses using the 2D finite element method. Parameter analyses for various types of input motions infer that pulse type waves are crucial to amplification of response of the base-isolated structure with damaged piles, due to lateral large displacement from the surrounding liquefied soil.