Tsunami overflow may destroy the coast-protection structures through continuous scour behind them. In this paper, the incompressible smoothed particle hydrodynamics (ISPH) method [Gotoh, H., Khayyer, A., Ikari, H., Arikawa, T. & Shimosako, K. [2014] “On enhancement of incompressible SPH method for simulation of violent sloshing flows,” Appl. Ocean Res. 46, 104–115.] is modified for simulation of erosion process behind the seawall under continuous tsunami overflow. Concepts of numerical turbid water particle (TWP) and clear water particle (CWP) are proposed to deal with the sediment-entrained flow. Reasonable value of 1250 kg/m3 is suggested for the initial density of the TWPs based on studies of bottom sediment movement. Sediment particle is judged to initiate its movement if the exerting shear stress exceeds the critical shear stress (CSS) of incipient motion of sediment calculated from a prescribed formula. The numerical results are compared with the data of flume experiment [Arikawa, T., Ikeda, T., Kubota, K. [2014] “Experimental study on scour behind seawall due to tsunami overflow,” J. Jpn. Soc. Civil Eng., Ser. B2 (Coastal Eng.) 70 (2), I_926-I_930 (in Japanese).]. The predicted results of the maximum depth as well as the shape of the scour pit reasonably agree with the experimental data.