In this paper, the indirect boundary integral equation method (BIEM) is applied to the 3D analysis of an electromagnetic system with a time-varying excitation in the presence of material motion. To do this, a fundamental Green's function for the convection-diffusion equation is derived. Using the Green's function, both effects of the time-varying magnetic field and the material motion are reflected on numerical solutions. The integral representation of the eddy current and the electromagnetic force is developed in terms of the equivalent magnetic surface current density and the equivalent magnetic surface charge density. The validity of the proposed method is examined by comparing the numerical results of the magnetic levitation force with the experimental values.