A new discrete non-reflecting boundary condition for the time-dependent Maxwell equations describing the propagation of an electromagnetic wave in an infinite homogenous lossless rectangular waveguide with perfectly conducting walls is presented. It is derived from a virtual spatial finite difference discretization of the problem on the unbounded domain. Fourier transforms are used to decouple transversal modes. A judicious combination of edge based nodal values permits us to recover a simple structure in the Laplace domain. Using this, it is possible to approximate the convolution in time by a similar fast convolution algorithm as for the standard wave equation.