Absorbing boundary conditions are presented for three-dimensional time-dependent Schrödinger-type of equations as a means to reduce the cost of the quantum-mechanical calculations. The boundary condition is first derived from a semidiscrete approximation of the Schrödinger equation with the advantage that the resulting formulas are automatically compatible with the finite-difference scheme and no further discretization is needed in space. The absorbing boundary condition is expressed as a discrete Dirichlet-to-Neumann map, which can be further approximated in time by using rational approximations of the Laplace transform to enable a more efficient implementation. This approach can be applied to domains with arbitrary geometry. The stability of the zeroth-order and first-order absorbing boundary conditions is proved. We tested the boundary conditions on benchmark problems. The effectiveness is further verified by a time-dependent Hartree-Fock model with Skyrme interactions. The accuracy in terms of energy and nucleon density is examined as well.