A systematic manner of deriving physically self-consistent, time-dependent boundary equations for MHD initial boundary problems is presented. The formulation is based on the use of the method of projected characteristics described in Paper I. It is shown that the full use of the compatibility equations (differential equations relating variations at two spatial locations and times) is required in determining the time-dependent boundary conditions. To provide a clear physical picture as an example, the evolution of axisymmetric global magnetic field by photospheric differential rotation is considered. The details of the formulation are described together with other considerations - in particular, the possible cause of the observed time difference for the reversal of the polar magnetic field on the Sun.