Characteristics of an ultrasonic suction pump that uses a vibrating piston surface and a pipe are numerically simulated and compared with experimental results. Fluid analysis based on the finite-difference time-domain (FDTD) routine is performed, where the nonlinear term and the moving fluid–surface boundary condition are considered. As a result, the suction mechanism of the pump is found to be similar to that of a check valve, where the gap is open during the inflow phase, and it is nearly closed during the outflow phase. The effects of Reynolds number, vibration amplitude and gap thickness on the pump performance are analyzed. The calculated result is in good agreement with the previously measured results.